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

Comparing:
branches/development/src/nonbonded/Electrostatic.cpp (file contents), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
trunk/src/nonbonded/Electrostatic.cpp (file contents), Revision 1921 by gezelter, Thu Aug 1 18:23:07 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		#include <stdio.h>
44		#include <string.h>
45
46		#include <cmath>
47	+	#include <numeric>
48		#include "nonbonded/Electrostatic.hpp"
49		#include "utils/simError.h"
50		#include "types/NonBondedInteractionType.hpp"
51	<	#include "types/DirectionalAtomType.hpp"
51	>	#include "types/FixedChargeAdapter.hpp"
52	>	#include "types/FluctuatingChargeAdapter.hpp"
53	>	#include "types/MultipoleAdapter.hpp"
54	>	#include "io/Globals.hpp"
55	>	#include "nonbonded/SlaterIntegrals.hpp"
56	>	#include "utils/PhysicalConstants.hpp"
57	>	#include "math/erfc.hpp"
58	>	#include "math/SquareMatrix.hpp"
59	>	#include "primitives/Molecule.hpp"
60
61
62		namespace OpenMD {
63
64		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
65	<	forceField_(NULL) {}
65	>	forceField_(NULL), info_(NULL),
66	>	haveCutoffRadius_(false),
67	>	haveDampingAlpha_(false),
68	>	haveDielectric_(false),
69	>	haveElectroSplines_(false)
70	>	{}
71
72		void Electrostatic::initialize() {
73	+
74	+	Globals* simParams_ = info_->getSimParams();
75	+
76	+	summationMap_["HARD"]               = esm_HARD;
77	+	summationMap_["NONE"]               = esm_HARD;
78	+	summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
79	+	summationMap_["SHIFTED_POTENTIAL"]  = esm_SHIFTED_POTENTIAL;
80	+	summationMap_["SHIFTED_FORCE"]      = esm_SHIFTED_FORCE;
81	+	summationMap_["TAYLOR_SHIFTED"]     = esm_TAYLOR_SHIFTED;
82	+	summationMap_["REACTION_FIELD"]     = esm_REACTION_FIELD;
83	+	summationMap_["EWALD_FULL"]         = esm_EWALD_FULL;
84	+	summationMap_["EWALD_PME"]          = esm_EWALD_PME;
85	+	summationMap_["EWALD_SPME"]         = esm_EWALD_SPME;
86	+	screeningMap_["DAMPED"]             = DAMPED;
87	+	screeningMap_["UNDAMPED"]           = UNDAMPED;
88	+
89		// these prefactors convert the multipole interactions into kcal / mol
90		// all were computed assuming distances are measured in angstroms
91		// Charge-Charge, assuming charges are measured in electrons
#	Line 62 | Line 93 | namespace OpenMD {
93		// Charge-Dipole, assuming charges are measured in electrons, and
94		// dipoles are measured in debyes
95		pre12_ = 69.13373;
96	<	// Dipole-Dipole, assuming dipoles are measured in debyes
96	>	// Dipole-Dipole, assuming dipoles are measured in Debye
97		pre22_ = 14.39325;
98		// Charge-Quadrupole, assuming charges are measured in electrons, and
99		// quadrupoles are measured in 10^-26 esu cm^2
100	<	// This unit is also known affectionately as an esu centi-barn.
100	>	// This unit is also known affectionately as an esu centibarn.
101		pre14_ = 69.13373;
102	<
102	>	// Dipole-Quadrupole, assuming dipoles are measured in debyes and
103	>	// quadrupoles in esu centibarns:
104	>	pre24_ = 14.39325;
105	>	// Quadrupole-Quadrupole, assuming esu centibarns:
106	>	pre44_ = 14.39325;
107	>
108		// conversions for the simulation box dipole moment
109		chargeToC_ = 1.60217733e-19;
110		angstromToM_ = 1.0e-10;
111		debyeToCm_ = 3.33564095198e-30;
112
113	<	// number of points for electrostatic splines
113	>	// Default number of points for electrostatic splines
114		np_ = 100;
115
116		// variables to handle different summation methods for long-range
117		// electrostatics:
118	<	summationMethod_ = NONE;
118	>	summationMethod_ = esm_HARD;
119		screeningMethod_ = UNDAMPED;
120		dielectric_ = 1.0;
85	–	one_third_ = 1.0 / 3.0;
86	–	haveDefaultCutoff_ = false;
87	–	haveDampingAlpha_ = false;
88	–	haveDielectric_ = false;
89	–	haveElectroSpline_ = false;
121
122	<	// find all of the Electrostatic atom Types:
123	<	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
124	<	ForceField::AtomTypeContainer::MapTypeIterator i;
125	<	AtomType* at;
126	<
127	<	for (at = atomTypes->beginType(i); at != NULL;
128	<	at = atomTypes->nextType(i)) {
129	<
130	<	if (at->isElectrostatic())
131	<	addType(at);
122	>	// check the summation method:
123	>	if (simParams_->haveElectrostaticSummationMethod()) {
124	>	string myMethod = simParams_->getElectrostaticSummationMethod();
125	>	toUpper(myMethod);
126	>	map<string, ElectrostaticSummationMethod>::iterator i;
127	>	i = summationMap_.find(myMethod);
128	>	if ( i != summationMap_.end() ) {
129	>	summationMethod_ = (*i).second;
130	>	} else {
131	>	// throw error
132	>	sprintf( painCave.errMsg,
133	>	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
134	>	"\t(Input file specified %s .)\n"
135	>	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
136	>	"\t\"shifted_potential\", \"shifted_force\",\n"
137	>	"\t\"taylor_shifted\", or \"reaction_field\".\n",
138	>	myMethod.c_str() );
139	>	painCave.isFatal = 1;
140	>	simError();
141	>	}
142	>	} else {
143	>	// set ElectrostaticSummationMethod to the cutoffMethod:
144	>	if (simParams_->haveCutoffMethod()){
145	>	string myMethod = simParams_->getCutoffMethod();
146	>	toUpper(myMethod);
147	>	map<string, ElectrostaticSummationMethod>::iterator i;
148	>	i = summationMap_.find(myMethod);
149	>	if ( i != summationMap_.end() ) {
150	>	summationMethod_ = (*i).second;
151	>	}
152	>	}
153		}
154
155	+	if (summationMethod_ == esm_REACTION_FIELD) {
156	+	if (!simParams_->haveDielectric()) {
157	+	// throw warning
158	+	sprintf( painCave.errMsg,
159	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
160	+	"\tA default value of %f will be used for the dielectric.\n", dielectric_);
161	+	painCave.isFatal = 0;
162	+	painCave.severity = OPENMD_INFO;
163	+	simError();
164	+	} else {
165	+	dielectric_ = simParams_->getDielectric();
166	+	}
167	+	haveDielectric_ = true;
168	+	}
169	+
170	+	if (simParams_->haveElectrostaticScreeningMethod()) {
171	+	string myScreen = simParams_->getElectrostaticScreeningMethod();
172	+	toUpper(myScreen);
173	+	map<string, ElectrostaticScreeningMethod>::iterator i;
174	+	i = screeningMap_.find(myScreen);
175	+	if ( i != screeningMap_.end()) {
176	+	screeningMethod_ = (*i).second;
177	+	} else {
178	+	sprintf( painCave.errMsg,
179	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
180	+	"\t(Input file specified %s .)\n"
181	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
182	+	"or \"damped\".\n", myScreen.c_str() );
183	+	painCave.isFatal = 1;
184	+	simError();
185	+	}
186	+	}
187	+
188		// check to make sure a cutoff value has been set:
189	<	if (!haveDefaultCutoff_) {
189	>	if (!haveCutoffRadius_) {
190		sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
191		"Cutoff value!\n");
192		painCave.severity = OPENMD_ERROR;
193		painCave.isFatal = 1;
194		simError();
195		}
196	<
197	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
198	<	rcuti_ = 1.0 / defaultCutoff_;
199	<	rcuti2_ = rcuti_ * rcuti_;
200	<	rcuti3_ = rcuti2_ * rcuti_;
201	<	rcuti4_ = rcuti2_ * rcuti2_;
202	<
203	<	if (screeningMethod_ == DAMPED) {
204	<	if (!haveDampingAlpha_) {
205	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no "
206	<	"DampingAlpha value!\n");
207	<	painCave.severity = OPENMD_ERROR;
208	<	painCave.isFatal = 1;
196	>
197	>	if (screeningMethod_ == DAMPED || summationMethod_ == esm_EWALD_FULL) {
198	>	if (!simParams_->haveDampingAlpha()) {
199	>	// first set a cutoff dependent alpha value
200	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
201	>	dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
202	>	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
203	>	// throw warning
204	>	sprintf( painCave.errMsg,
205	>	"Electrostatic::initialize: dampingAlpha was not specified in the\n"
206	>	"\tinput file.  A default value of %f (1/ang) will be used for the\n"
207	>	"\tcutoff of %f (ang).\n",
208	>	dampingAlpha_, cutoffRadius_);
209	>	painCave.severity = OPENMD_INFO;
210	>	painCave.isFatal = 0;
211		simError();
212	+	} else {
213	+	dampingAlpha_ = simParams_->getDampingAlpha();
214		}
215	+	haveDampingAlpha_ = true;
216	+	}
217
127	–	alpha2_ = dampingAlpha_ * dampingAlpha_;
128	–	alpha4_ = alpha2_ * alpha2_;
129	–	alpha6_ = alpha4_ * alpha2_;
130	–	alpha8_ = alpha4_ * alpha4_;
131	–
132	–	constEXP_ = exp(-alpha2_ * defaultCutoff2_);
133	–	invRootPi_ = 0.56418958354775628695;
134	–	alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
218
219	<	c1c_ = erfc(dampingAlpha_ * defaultCutoff_) * rcuti_;
220	<	c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
221	<	c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
222	<	c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
223	<	c5c_ = 8.0 * alphaPi_ * alpha6_ + 7.0 * c4c_ * rcuti2_;
224	<	c6c_ = 16.0 * alphaPi_ * alpha8_ + 9.0 * c5c_ * rcuti2_;
219	>	Etypes.clear();
220	>	Etids.clear();
221	>	FQtypes.clear();
222	>	FQtids.clear();
223	>	ElectrostaticMap.clear();
224	>	Jij.clear();
225	>	nElectro_ = 0;
226	>	nFlucq_ = 0;
227	>
228	>	Etids.resize( forceField_->getNAtomType(), -1);
229	>	FQtids.resize( forceField_->getNAtomType(), -1);
230	>
231	>	set<AtomType*>::iterator at;
232	>	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
233	>	if ((*at)->isElectrostatic()) nElectro_++;
234	>	if ((*at)->isFluctuatingCharge()) nFlucq_++;
235	>	}
236	>
237	>	Jij.resize(nFlucq_);
238	>
239	>	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
240	>	if ((*at)->isElectrostatic()) addType(*at);
241	>	}
242	>
243	>	if (summationMethod_ == esm_REACTION_FIELD) {
244	>	preRF_ = (dielectric_ - 1.0) /
245	>	((2.0 * dielectric_ + 1.0) * pow(cutoffRadius_,3) );
246	>	}
247	>
248	>	RealType b0c, b1c, b2c, b3c, b4c, b5c;
249	>	RealType db0c_1, db0c_2, db0c_3, db0c_4, db0c_5;
250	>	RealType a2, expTerm, invArootPi;
251	>
252	>	RealType r = cutoffRadius_;
253	>	RealType r2 = r * r;
254	>	RealType ric = 1.0 / r;
255	>	RealType ric2 = ric * ric;
256	>
257	>	if (screeningMethod_ == DAMPED) {
258	>	a2 = dampingAlpha_ * dampingAlpha_;
259	>	invArootPi = 1.0 / (dampingAlpha_ * sqrt(M_PI));
260	>	expTerm = exp(-a2 * r2);
261	>	// values of Smith's B_l functions at the cutoff radius:
262	>	b0c = erfc(dampingAlpha_ * r) / r;
263	>	b1c = (      b0c     + 2.0*a2     * expTerm * invArootPi) / r2;
264	>	b2c = (3.0 * b1c + pow(2.0*a2, 2) * expTerm * invArootPi) / r2;
265	>	b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2;
266	>	b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2;
267	>	b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2;
268	>	// Half the Smith self piece:
269	>	selfMult1_ = - a2 * invArootPi;
270	>	selfMult2_ = - 2.0 * a2 * a2 * invArootPi / 3.0;
271	>	selfMult4_ = - 4.0 * a2 * a2 * a2 * invArootPi / 5.0;
272		} else {
273	<	c1c_ = rcuti_;
274	<	c2c_ = c1c_ * rcuti_;
275	<	c3c_ = 3.0 * c2c_ * rcuti_;
276	<	c4c_ = 5.0 * c3c_ * rcuti2_;
277	<	c5c_ = 7.0 * c4c_ * rcuti2_;
278	<	c6c_ = 9.0 * c5c_ * rcuti2_;
273	>	a2 = 0.0;
274	>	b0c = 1.0 / r;
275	>	b1c = (      b0c) / r2;
276	>	b2c = (3.0 * b1c) / r2;
277	>	b3c = (5.0 * b2c) / r2;
278	>	b4c = (7.0 * b3c) / r2;
279	>	b5c = (9.0 * b4c) / r2;
280	>	selfMult1_ = 0.0;
281	>	selfMult2_ = 0.0;
282	>	selfMult4_ = 0.0;
283		}
284	<
285	<	if (summationMethod_ == REACTION_FIELD) {
286	<	if (haveDielectric_) {
287	<	preRF_ = (dielectric_ - 1.0) /
288	<	((2.0 * dielectric_ + 1.0) * defaultCutoff2_ * defaultCutoff_);
289	<	preRF2_ = 2.0 * preRF_;
284	>
285	>	// higher derivatives of B_0 at the cutoff radius:
286	>	db0c_1 = -r * b1c;
287	>	db0c_2 =     -b1c + r2 * b2c;
288	>	db0c_3 =          3.0*r*b2c  - r2*r*b3c;
289	>	db0c_4 =          3.0*b2c  - 6.0*r2*b3c     + r2*r2*b4c;
290	>	db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;
291	>
292	>	if (summationMethod_ == esm_EWALD_FULL) {
293	>	selfMult1_ *= 2.0;
294	>	selfMult2_ *= 2.0;
295	>	selfMult4_ *= 2.0;
296	>	} else {
297	>	selfMult1_ -= b0c;
298	>	selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
299	>	selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
300	>	}
301	>
302	>	// working variables for the splines:
303	>	RealType ri, ri2;
304	>	RealType b0, b1, b2, b3, b4, b5;
305	>	RealType db0_1, db0_2, db0_3, db0_4, db0_5;
306	>	RealType f, fc, f0;
307	>	RealType g, gc, g0, g1, g2, g3, g4;
308	>	RealType h, hc, h1, h2, h3, h4;
309	>	RealType s, sc, s2, s3, s4;
310	>	RealType t, tc, t3, t4;
311	>	RealType u, uc, u4;
312	>
313	>	// working variables for Taylor expansion:
314	>	RealType rmRc, rmRc2, rmRc3, rmRc4;
315	>
316	>	// Approximate using splines using a maximum of 0.1 Angstroms
317	>	// between points.
318	>	int nptest = int((cutoffRadius_ + 2.0) / 0.1);
319	>	np_ = (np_ > nptest) ? np_ : nptest;
320	>
321	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
322	>	// have charged atoms longer than the cutoffRadius away from each
323	>	// other.  Splining is almost certainly the best choice here.
324	>	// Direct calls to erfc would be preferrable if it is a very fast
325	>	// implementation.
326	>
327	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_);
328	>
329	>	// Storage vectors for the computed functions
330	>	vector<RealType> rv;
331	>	vector<RealType> v01v;
332	>	vector<RealType> v11v;
333	>	vector<RealType> v21v, v22v;
334	>	vector<RealType> v31v, v32v;
335	>	vector<RealType> v41v, v42v, v43v;
336	>
337	>	for (int i = 1; i < np_ + 1; i++) {
338	>	r = RealType(i) * dx;
339	>	rv.push_back(r);
340	>
341	>	ri = 1.0 / r;
342	>	ri2 = ri * ri;
343	>
344	>	r2 = r * r;
345	>	expTerm = exp(-a2 * r2);
346	>
347	>	// Taylor expansion factors (no need for factorials this way):
348	>	rmRc = r - cutoffRadius_;
349	>	rmRc2 = rmRc  * rmRc / 2.0;
350	>	rmRc3 = rmRc2 * rmRc / 3.0;
351	>	rmRc4 = rmRc3 * rmRc / 4.0;
352	>
353	>	// values of Smith's B_l functions at r:
354	>	if (screeningMethod_ == DAMPED) {
355	>	b0 = erfc(dampingAlpha_ * r) * ri;
356	>	b1 = (      b0 +     2.0*a2     * expTerm * invArootPi) * ri2;
357	>	b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2;
358	>	b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2;
359	>	b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2;
360	>	b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2;
361		} else {
362	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no Dielectric"
363	<	" value!\n");
364	<	painCave.severity = OPENMD_ERROR;
362	>	b0 = ri;
363	>	b1 = (      b0) * ri2;
364	>	b2 = (3.0 * b1) * ri2;
365	>	b3 = (5.0 * b2) * ri2;
366	>	b4 = (7.0 * b3) * ri2;
367	>	b5 = (9.0 * b4) * ri2;
368	>	}
369	>
370	>	// higher derivatives of B_0 at r:
371	>	db0_1 = -r * b1;
372	>	db0_2 =     -b1 + r2 * b2;
373	>	db0_3 =          3.0*r*b2   - r2*r*b3;
374	>	db0_4 =          3.0*b2   - 6.0*r2*b3     + r2*r2*b4;
375	>	db0_5 =                    -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5;
376	>
377	>	f = b0;
378	>	fc = b0c;
379	>	f0 = f - fc - rmRc*db0c_1;
380	>
381	>	g = db0_1;
382	>	gc = db0c_1;
383	>	g0 = g - gc;
384	>	g1 = g0 - rmRc *db0c_2;
385	>	g2 = g1 - rmRc2*db0c_3;
386	>	g3 = g2 - rmRc3*db0c_4;
387	>	g4 = g3 - rmRc4*db0c_5;
388	>
389	>	h = db0_2;
390	>	hc = db0c_2;
391	>	h1 = h - hc;
392	>	h2 = h1 - rmRc *db0c_3;
393	>	h3 = h2 - rmRc2*db0c_4;
394	>	h4 = h3 - rmRc3*db0c_5;
395	>
396	>	s = db0_3;
397	>	sc = db0c_3;
398	>	s2 = s - sc;
399	>	s3 = s2 - rmRc *db0c_4;
400	>	s4 = s3 - rmRc2*db0c_5;
401	>
402	>	t = db0_4;
403	>	tc = db0c_4;
404	>	t3 = t - tc;
405	>	t4 = t3 - rmRc *db0c_5;
406	>
407	>	u = db0_5;
408	>	uc = db0c_5;
409	>	u4 = u - uc;
410	>
411	>	// in what follows below, the various v functions are used for
412	>	// potentials and torques, while the w functions show up in the
413	>	// forces.
414	>
415	>	switch (summationMethod_) {
416	>	case esm_SHIFTED_FORCE:
417	>
418	>	v01 = f - fc - rmRc*gc;
419	>	v11 = g - gc - rmRc*hc;
420	>	v21 = g*ri - gc*ric - rmRc*(hc - gc*ric)*ric;
421	>	v22 = h - g*ri - (hc - gc*ric) - rmRc*(sc - (hc - gc*ric)*ric);
422	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric - rmRc*(sc-2.0*(hc-gc*ric)*ric)*ric;
423	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric)
424	>	- rmRc*(tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
425	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2
426	>	- rmRc*(sc - 3.0*(hc-gc*ric)*ric)*ric2;
427	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric
428	>	- rmRc*(tc - (4.0*sc - 9.0*(hc - gc*ric)*ric)*ric)*ric;
429	>
430	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
431	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric)
432	>	- rmRc*(uc-3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
433	>
434	>	dv01 = g - gc;
435	>	dv11 = h - hc;
436	>	dv21 = (h - g*ri)*ri - (hc - gc*ric)*ric;
437	>	dv22 = (s - (h - g*ri)*ri) - (sc - (hc - gc*ric)*ric);
438	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri - (sc - 2.0*(hc-gc*ric)*ric)*ric;
439	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri)
440	>	- (tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
441	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2 - (sc - 3.0*(hc - gc*ric)*ric)*ric2;
442	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri
443	>	- (tc - (4.0*sc - 9.0*(hc-gc*ric)*ric)*ric)*ric;
444	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri)
445	>	- (uc - 3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
446	>
447	>	break;
448	>
449	>	case esm_TAYLOR_SHIFTED:
450	>
451	>	v01 = f0;
452	>	v11 = g1;
453	>	v21 = g2 * ri;
454	>	v22 = h2 - v21;
455	>	v31 = (h3 - g3 * ri) * ri;
456	>	v32 = s3 - 3.0*v31;
457	>	v41 = (h4 - g4 * ri) * ri2;
458	>	v42 = s4 * ri - 3.0*v41;
459	>	v43 = t4 - 6.0*v42 - 3.0*v41;
460	>
461	>	dv01 = g0;
462	>	dv11 = h1;
463	>	dv21 = (h2 - g2*ri)*ri;
464	>	dv22 = (s2 - (h2 - g2*ri)*ri);
465	>	dv31 = (s3 - 2.0*(h3-g3*ri)*ri)*ri;
466	>	dv32 = (t3 - 3.0*(s3-2.0*(h3-g3*ri)*ri)*ri);
467	>	dv41 = (s4 - 3.0*(h4 - g4*ri)*ri)*ri2;
468	>	dv42 = (t4 - (4.0*s4 - 9.0*(h4-g4*ri)*ri)*ri)*ri;
469	>	dv43 = (u4 - 3.0*(2.0*t4 - (7.0*s4 - 15.0*(h4 - g4*ri)*ri)*ri)*ri);
470	>
471	>	break;
472	>
473	>	case esm_SHIFTED_POTENTIAL:
474	>
475	>	v01 = f - fc;
476	>	v11 = g - gc;
477	>	v21 = g*ri - gc*ric;
478	>	v22 = h - g*ri - (hc - gc*ric);
479	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
480	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
481	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
482	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
483	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
484	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
485	>
486	>	dv01 = g;
487	>	dv11 = h;
488	>	dv21 = (h - g*ri)*ri;
489	>	dv22 = (s - (h - g*ri)*ri);
490	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
491	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
492	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
493	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
494	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
495	>
496	>	break;
497	>
498	>	case esm_SWITCHING_FUNCTION:
499	>	case esm_HARD:
500	>	case esm_EWALD_FULL:
501	>
502	>	v01 = f;
503	>	v11 = g;
504	>	v21 = g*ri;
505	>	v22 = h - g*ri;
506	>	v31 = (h-g*ri)*ri;
507	>	v32 = (s - 3.0*(h-g*ri)*ri);
508	>	v41 = (h - g*ri)*ri2;
509	>	v42 = (s-3.0*(h-g*ri)*ri)*ri;
510	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri);
511	>
512	>	dv01 = g;
513	>	dv11 = h;
514	>	dv21 = (h - g*ri)*ri;
515	>	dv22 = (s - (h - g*ri)*ri);
516	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
517	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
518	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
519	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
520	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
521	>
522	>	break;
523	>
524	>	case esm_REACTION_FIELD:
525	>
526	>	// following DL_POLY's lead for shifting the image charge potential:
527	>	f = b0 + preRF_ * r2;
528	>	fc = b0c + preRF_ * cutoffRadius_ * cutoffRadius_;
529	>
530	>	g = db0_1 + preRF_ * 2.0 * r;
531	>	gc = db0c_1 + preRF_ * 2.0 * cutoffRadius_;
532	>
533	>	h = db0_2 + preRF_ * 2.0;
534	>	hc = db0c_2 + preRF_ * 2.0;
535	>
536	>	v01 = f - fc;
537	>	v11 = g - gc;
538	>	v21 = g*ri - gc*ric;
539	>	v22 = h - g*ri - (hc - gc*ric);
540	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
541	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
542	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
543	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
544	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
545	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
546	>
547	>	dv01 = g;
548	>	dv11 = h;
549	>	dv21 = (h - g*ri)*ri;
550	>	dv22 = (s - (h - g*ri)*ri);
551	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
552	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
553	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
554	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
555	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
556	>
557	>	break;
558	>
559	>	case esm_EWALD_PME:
560	>	case esm_EWALD_SPME:
561	>	default :
562	>	map<string, ElectrostaticSummationMethod>::iterator i;
563	>	std::string meth;
564	>	for (i = summationMap_.begin(); i != summationMap_.end(); ++i) {
565	>	if ((*i).second == summationMethod_) meth = (*i).first;
566	>	}
567	>	sprintf( painCave.errMsg,
568	>	"Electrostatic::initialize: electrostaticSummationMethod %s \n"
569	>	"\thas not been implemented yet. Please select one of:\n"
570	>	"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n",
571	>	meth.c_str() );
572		painCave.isFatal = 1;
573		simError();
574	+	break;
575		}
576	+
577	+	// Add these computed values to the storage vectors for spline creation:
578	+	v01v.push_back(v01);
579	+	v11v.push_back(v11);
580	+	v21v.push_back(v21);
581	+	v22v.push_back(v22);
582	+	v31v.push_back(v31);
583	+	v32v.push_back(v32);
584	+	v41v.push_back(v41);
585	+	v42v.push_back(v42);
586	+	v43v.push_back(v43);
587		}
164	–
165	–	RealType dx = defaultCutoff_ / RealType(np_ - 1);
166	–	RealType rval;
167	–	vector<RealType> rvals;
168	–	vector<RealType> yvals;
169	–	for (int i = 0; i < np_; i++) {
170	–	rval = RealType(i) * dx;
171	–	rvals.push_back(rval);
172	–	yvals.push_back(erfc(dampingAlpha_ * rval));
173	–	}
174	–	erfcSpline_ = new CubicSpline();
175	–	erfcSpline_->addPoints(rvals, yvals);
176	–	haveElectroSpline_ = true;
588
589	+	// construct the spline structures and fill them with the values we've
590	+	// computed:
591	+
592	+	v01s = new CubicSpline();
593	+	v01s->addPoints(rv, v01v);
594	+	v11s = new CubicSpline();
595	+	v11s->addPoints(rv, v11v);
596	+	v21s = new CubicSpline();
597	+	v21s->addPoints(rv, v21v);
598	+	v22s = new CubicSpline();
599	+	v22s->addPoints(rv, v22v);
600	+	v31s = new CubicSpline();
601	+	v31s->addPoints(rv, v31v);
602	+	v32s = new CubicSpline();
603	+	v32s->addPoints(rv, v32v);
604	+	v41s = new CubicSpline();
605	+	v41s->addPoints(rv, v41v);
606	+	v42s = new CubicSpline();
607	+	v42s->addPoints(rv, v42v);
608	+	v43s = new CubicSpline();
609	+	v43s->addPoints(rv, v43v);
610	+
611	+	haveElectroSplines_ = true;
612	+
613		initialized_ = true;
614		}
615
616		void Electrostatic::addType(AtomType* atomType){
617	<
617	>
618		ElectrostaticAtomData electrostaticAtomData;
619		electrostaticAtomData.is_Charge = false;
620		electrostaticAtomData.is_Dipole = false;
186	–	electrostaticAtomData.is_SplitDipole = false;
621		electrostaticAtomData.is_Quadrupole = false;
622	+	electrostaticAtomData.is_Fluctuating = false;
623
624	<	if (atomType->isCharge()) {
190	<	GenericData* data = atomType->getPropertyByName("Charge");
624	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
625
626	<	if (data == NULL) {
193	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
194	<	"Charge\n"
195	<	"\tparameters for atomType %s.\n",
196	<	atomType->getName().c_str());
197	<	painCave.severity = OPENMD_ERROR;
198	<	painCave.isFatal = 1;
199	<	simError();
200	<	}
201	<
202	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
203	<	if (doubleData == NULL) {
204	<	sprintf( painCave.errMsg,
205	<	"Electrostatic::addType could not convert GenericData to "
206	<	"Charge for\n"
207	<	"\tatom type %s\n", atomType->getName().c_str());
208	<	painCave.severity = OPENMD_ERROR;
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
626	>	if (fca.isFixedCharge()) {
627		electrostaticAtomData.is_Charge = true;
628	<	electrostaticAtomData.charge = doubleData->getData();
628	>	electrostaticAtomData.fixedCharge = fca.getCharge();
629		}
630
631	<	if (atomType->isDirectional()) {
632	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
633	<
219	<	if (daType->isDipole()) {
220	<	GenericData* data = daType->getPropertyByName("Dipole");
221	<
222	<	if (data == NULL) {
223	<	sprintf( painCave.errMsg,
224	<	"Electrostatic::addType could not find Dipole\n"
225	<	"\tparameters for atomType %s.\n",
226	<	daType->getName().c_str());
227	<	painCave.severity = OPENMD_ERROR;
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
231	<
232	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
233	<	if (doubleData == NULL) {
234	<	sprintf( painCave.errMsg,
235	<	"Electrostatic::addType could not convert GenericData to "
236	<	"Dipole Moment\n"
237	<	"\tfor atom type %s\n", daType->getName().c_str());
238	<	painCave.severity = OPENMD_ERROR;
239	<	painCave.isFatal = 1;
240	<	simError();
241	<	}
631	>	MultipoleAdapter ma = MultipoleAdapter(atomType);
632	>	if (ma.isMultipole()) {
633	>	if (ma.isDipole()) {
634		electrostaticAtomData.is_Dipole = true;
635	<	electrostaticAtomData.dipole_moment = doubleData->getData();
635	>	electrostaticAtomData.dipole = ma.getDipole();
636		}
637	<
246	<	if (daType->isSplitDipole()) {
247	<	GenericData* data = daType->getPropertyByName("SplitDipoleDistance");
248	<
249	<	if (data == NULL) {
250	<	sprintf(painCave.errMsg,
251	<	"Electrostatic::addType could not find SplitDipoleDistance\n"
252	<	"\tparameter for atomType %s.\n",
253	<	daType->getName().c_str());
254	<	painCave.severity = OPENMD_ERROR;
255	<	painCave.isFatal = 1;
256	<	simError();
257	<	}
258	<
259	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
260	<	if (doubleData == NULL) {
261	<	sprintf( painCave.errMsg,
262	<	"Electrostatic::addType could not convert GenericData to "
263	<	"SplitDipoleDistance for\n"
264	<	"\tatom type %s\n", daType->getName().c_str());
265	<	painCave.severity = OPENMD_ERROR;
266	<	painCave.isFatal = 1;
267	<	simError();
268	<	}
269	<	electrostaticAtomData.is_SplitDipole = true;
270	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
271	<	}
272	<
273	<	if (daType->isQuadrupole()) {
274	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
275	<
276	<	if (data == NULL) {
277	<	sprintf( painCave.errMsg,
278	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
279	<	"\tparameter for atomType %s.\n",
280	<	daType->getName().c_str());
281	<	painCave.severity = OPENMD_ERROR;
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
286	<	// Quadrupoles in OpenMD are set as the diagonal elements
287	<	// of the diagonalized traceless quadrupole moment tensor.
288	<	// The column vectors of the unitary matrix that diagonalizes
289	<	// the quadrupole moment tensor become the eFrame (or the
290	<	// electrostatic version of the body-fixed frame.
291	<
292	<	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
293	<	if (v3dData == NULL) {
294	<	sprintf( painCave.errMsg,
295	<	"Electrostatic::addType could not convert GenericData to "
296	<	"Quadrupole Moments for\n"
297	<	"\tatom type %s\n", daType->getName().c_str());
298	<	painCave.severity = OPENMD_ERROR;
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
637	>	if (ma.isQuadrupole()) {
638		electrostaticAtomData.is_Quadrupole = true;
639	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
639	>	electrostaticAtomData.quadrupole = ma.getQuadrupole();
640		}
641		}
642
643	<	AtomTypeProperties atp = atomType->getATP();
643	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
644
645	<	pair<map<int,AtomType*>::iterator,bool> ret;
646	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
645	>	if (fqa.isFluctuatingCharge()) {
646	>	electrostaticAtomData.is_Fluctuating = true;
647	>	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
648	>	electrostaticAtomData.hardness = fqa.getHardness();
649	>	electrostaticAtomData.slaterN = fqa.getSlaterN();
650	>	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
651	>	}
652	>
653	>	int atid = atomType->getIdent();
654	>	int etid = Etypes.size();
655	>	int fqtid = FQtypes.size();
656	>
657	>	pair<set<int>::iterator,bool> ret;
658	>	ret = Etypes.insert( atid );
659		if (ret.second == false) {
660		sprintf( painCave.errMsg,
661		"Electrostatic already had a previous entry with ident %d\n",
662	<	atp.ident);
662	>	atid);
663		painCave.severity = OPENMD_INFO;
664		painCave.isFatal = 0;
665		simError();
666		}
667
668	<	ElectrostaticMap[atomType] = electrostaticAtomData;
668	>	Etids[ atid ] = etid;
669	>	ElectrostaticMap.push_back(electrostaticAtomData);
670	>
671	>	if (electrostaticAtomData.is_Fluctuating) {
672	>	ret = FQtypes.insert( atid );
673	>	if (ret.second == false) {
674	>	sprintf( painCave.errMsg,
675	>	"Electrostatic already had a previous fluctuating charge entry with ident %d\n",
676	>	atid );
677	>	painCave.severity = OPENMD_INFO;
678	>	painCave.isFatal = 0;
679	>	simError();
680	>	}
681	>	FQtids[atid] = fqtid;
682	>	Jij[fqtid].resize(nFlucq_);
683	>
684	>	// Now, iterate over all known fluctuating and add to the
685	>	// coulomb integral map:
686	>
687	>	std::set<int>::iterator it;
688	>	for( it = FQtypes.begin(); it != FQtypes.end(); ++it) {
689	>	int etid2 = Etids[ (*it) ];
690	>	int fqtid2 = FQtids[ (*it) ];
691	>	ElectrostaticAtomData eaData2 = ElectrostaticMap[ etid2 ];
692	>	RealType a = electrostaticAtomData.slaterZeta;
693	>	RealType b = eaData2.slaterZeta;
694	>	int m = electrostaticAtomData.slaterN;
695	>	int n = eaData2.slaterN;
696	>
697	>	// Create the spline of the coulombic integral for s-type
698	>	// Slater orbitals.  Add a 2 angstrom safety window to deal
699	>	// with cutoffGroups that have charged atoms longer than the
700	>	// cutoffRadius away from each other.
701	>
702	>	RealType rval;
703	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
704	>	vector<RealType> rvals;
705	>	vector<RealType> Jvals;
706	>	// don't start at i = 0, as rval = 0 is undefined for the
707	>	// slater overlap integrals.
708	>	for (int i = 1; i < np_+1; i++) {
709	>	rval = RealType(i) * dr;
710	>	rvals.push_back(rval);
711	>	Jvals.push_back(sSTOCoulInt( a, b, m, n, rval *
712	>	PhysicalConstants::angstromToBohr ) *
713	>	PhysicalConstants::hartreeToKcal );
714	>	}
715	>
716	>	CubicSpline* J = new CubicSpline();
717	>	J->addPoints(rvals, Jvals);
718	>	Jij[fqtid][fqtid2] = J;
719	>	Jij[fqtid2].resize( nFlucq_ );
720	>	Jij[fqtid2][fqtid] = J;
721	>	}
722	>	}
723		return;
724		}
725
726	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
727	<	RealType theRSW ) {
728	<	defaultCutoff_ = theECR;
327	<	rrf_ = defaultCutoff_;
328	<	rt_ = theRSW;
329	<	haveDefaultCutoff_ = true;
726	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
727	>	cutoffRadius_ = rCut;
728	>	haveCutoffRadius_ = true;
729		}
730	+
731		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
732		summationMethod_ = esm;
733		}
#	Line 343 | Line 743 | namespace OpenMD {
743		haveDielectric_ = true;
744		}
745
746	<	void Electrostatic::calcForce(InteractionData idat) {
746	>	void Electrostatic::calcForce(InteractionData &idat) {
747
348	–	// utility variables.  Should clean these up and use the Vector3d and
349	–	// Mat3x3d to replace as many as we can in future versions:
350	–
351	–	RealType q_i, q_j, mu_i, mu_j, d_i, d_j;
352	–	RealType qxx_i, qyy_i, qzz_i;
353	–	RealType qxx_j, qyy_j, qzz_j;
354	–	RealType cx_i, cy_i, cz_i;
355	–	RealType cx_j, cy_j, cz_j;
356	–	RealType cx2, cy2, cz2;
357	–	RealType ct_i, ct_j, ct_ij, a1;
358	–	RealType riji, ri, ri2, ri3, ri4;
359	–	RealType pref, vterm, epot, dudr;
360	–	RealType scale, sc2;
361	–	RealType pot_term, preVal, rfVal;
362	–	RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
363	–	RealType preSw, preSwSc;
364	–	RealType c1, c2, c3, c4;
365	–	RealType erfcVal, derfcVal;
366	–	RealType BigR;
367	–
368	–	Vector3d Q_i, Q_j;
369	–	Vector3d ux_i, uy_i, uz_i;
370	–	Vector3d ux_j, uy_j, uz_j;
371	–	Vector3d dudux_i, duduy_i, duduz_i;
372	–	Vector3d dudux_j, duduy_j, duduz_j;
373	–	Vector3d rhatdot2, rhatc4;
374	–	Vector3d dVdr;
375	–
376	–	pair<RealType, RealType> res;
377	–
748		if (!initialized_) initialize();
749
750	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
751	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
750	>	data1 = ElectrostaticMap[Etids[idat.atid1]];
751	>	data2 = ElectrostaticMap[Etids[idat.atid2]];
752	>
753	>	U = 0.0;  // Potential
754	>	F.zero();  // Force
755	>	Ta.zero(); // Torque on site a
756	>	Tb.zero(); // Torque on site b
757	>	Ea.zero(); // Electric field at site a
758	>	Eb.zero(); // Electric field at site b
759	>	dUdCa = 0.0; // fluctuating charge force at site a
760	>	dUdCb = 0.0; // fluctuating charge force at site a
761
762	<	// some variables we'll need independent of electrostatic type:
762	>	// Indirect interactions mediated by the reaction field.
763	>	indirect_Pot = 0.0;   // Potential
764	>	indirect_F.zero();    // Force
765	>	indirect_Ta.zero();   // Torque on site a
766	>	indirect_Tb.zero();   // Torque on site b
767
768	<	riji = 1.0 / idat.rij;
769	<	Vector3d rhat = idat.d  * riji;
768	>	// Excluded potential that is still computed for fluctuating charges
769	>	excluded_Pot= 0.0;
770
388	–	// logicals
771
772	<	bool i_is_Charge = data1.is_Charge;
391	<	bool i_is_Dipole = data1.is_Dipole;
392	<	bool i_is_SplitDipole = data1.is_SplitDipole;
393	<	bool i_is_Quadrupole = data1.is_Quadrupole;
772	>	// some variables we'll need independent of electrostatic type:
773
774	<	bool j_is_Charge = data2.is_Charge;
775	<	bool j_is_Dipole = data2.is_Dipole;
397	<	bool j_is_SplitDipole = data2.is_SplitDipole;
398	<	bool j_is_Quadrupole = data2.is_Quadrupole;
399	<
400	<	if (i_is_Charge)
401	<	q_i = data1.charge;
402	<
403	<	if (i_is_Dipole) {
404	<	mu_i = data1.dipole_moment;
405	<	uz_i = idat.eFrame1.getColumn(2);
774	>	ri = 1.0 /  *(idat.rij);
775	>	rhat =  *(idat.d)  * ri;
776
777	<	ct_i = dot(uz_i, rhat);
777	>	// logicals
778
779	<	if (i_is_SplitDipole)
780	<	d_i = data1.split_dipole_distance;
781	<
782	<	duduz_i = V3Zero;
413	<	}
414	<
415	<	if (i_is_Quadrupole) {
416	<	Q_i = data1.quadrupole_moments;
417	<	qxx_i = Q_i.x();
418	<	qyy_i = Q_i.y();
419	<	qzz_i = Q_i.z();
420	<
421	<	ux_i = idat.eFrame1.getColumn(0);
422	<	uy_i = idat.eFrame1.getColumn(1);
423	<	uz_i = idat.eFrame1.getColumn(2);
779	>	a_is_Charge = data1.is_Charge;
780	>	a_is_Dipole = data1.is_Dipole;
781	>	a_is_Quadrupole = data1.is_Quadrupole;
782	>	a_is_Fluctuating = data1.is_Fluctuating;
783
784	<	cx_i = dot(ux_i, rhat);
785	<	cy_i = dot(uy_i, rhat);
786	<	cz_i = dot(uz_i, rhat);
784	>	b_is_Charge = data2.is_Charge;
785	>	b_is_Dipole = data2.is_Dipole;
786	>	b_is_Quadrupole = data2.is_Quadrupole;
787	>	b_is_Fluctuating = data2.is_Fluctuating;
788
789	<	dudux_i = V3Zero;
790	<	duduy_i = V3Zero;
791	<	duduz_i = V3Zero;
789	>	// Obtain all of the required radial function values from the
790	>	// spline structures:
791	>
792	>	// needed for fields (and forces):
793	>	if (a_is_Charge || b_is_Charge) {
794	>	v01s->getValueAndDerivativeAt( *(idat.rij), v01, dv01);
795		}
796	+	if (a_is_Dipole || b_is_Dipole) {
797	+	v11s->getValueAndDerivativeAt( *(idat.rij), v11, dv11);
798	+	v11or = ri * v11;
799	+	}
800	+	if (a_is_Quadrupole || b_is_Quadrupole ||  (a_is_Dipole && b_is_Dipole)) {
801	+	v21s->getValueAndDerivativeAt( *(idat.rij), v21, dv21);
802	+	v22s->getValueAndDerivativeAt( *(idat.rij), v22, dv22);
803	+	v22or = ri * v22;
804	+	}
805
806	<	if (j_is_Charge)
807	<	q_j = data2.charge;
806	>	// needed for potentials (and forces and torques):
807	>	if ((a_is_Dipole && b_is_Quadrupole) ||
808	>	(b_is_Dipole && a_is_Quadrupole)) {
809	>	v31s->getValueAndDerivativeAt( *(idat.rij), v31, dv31);
810	>	v32s->getValueAndDerivativeAt( *(idat.rij), v32, dv32);
811	>	v31or = v31 * ri;
812	>	v32or = v32 * ri;
813	>	}
814	>	if (a_is_Quadrupole && b_is_Quadrupole) {
815	>	v41s->getValueAndDerivativeAt( *(idat.rij), v41, dv41);
816	>	v42s->getValueAndDerivativeAt( *(idat.rij), v42, dv42);
817	>	v43s->getValueAndDerivativeAt( *(idat.rij), v43, dv43);
818	>	v42or = v42 * ri;
819	>	v43or = v43 * ri;
820	>	}
821
822	<	if (j_is_Dipole) {
823	<	mu_j = data2.dipole_moment;
824	<	uz_j = idat.eFrame2.getColumn(2);
822	>	// calculate the single-site contributions (fields, etc).
823	>
824	>	if (a_is_Charge) {
825	>	C_a = data1.fixedCharge;
826
827	<	ct_j = dot(uz_j, rhat);
828	<
829	<	if (j_is_SplitDipole)
444	<	d_j = data2.split_dipole_distance;
827	>	if (a_is_Fluctuating) {
828	>	C_a += *(idat.flucQ1);
829	>	}
830
831	<	duduz_j = V3Zero;
831	>	if (idat.excluded) {
832	>	*(idat.skippedCharge2) += C_a;
833	>	} else {
834	>	// only do the field if we're not excluded:
835	>	Eb -= C_a *  pre11_ * dv01 * rhat;
836	>	}
837		}
838
839	<	if (j_is_Quadrupole) {
840	<	Q_j = data2.quadrupole_moments;
841	<	qxx_j = Q_j.x();
842	<	qyy_j = Q_j.y();
843	<	qzz_j = Q_j.z();
844	<
455	<	ux_j = idat.eFrame2.getColumn(0);
456	<	uy_j = idat.eFrame2.getColumn(1);
457	<	uz_j = idat.eFrame2.getColumn(2);
458	<
459	<	cx_j = dot(ux_j, rhat);
460	<	cy_j = dot(uy_j, rhat);
461	<	cz_j = dot(uz_j, rhat);
462	<
463	<	dudux_j = V3Zero;
464	<	duduy_j = V3Zero;
465	<	duduz_j = V3Zero;
839	>	if (a_is_Dipole) {
840	>	D_a = *(idat.dipole1);
841	>	rdDa = dot(rhat, D_a);
842	>	rxDa = cross(rhat, D_a);
843	>	if (!idat.excluded)
844	>	Eb -=  pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
845		}
846
847	<	epot = 0.0;
848	<	dVdr = V3Zero;
847	>	if (a_is_Quadrupole) {
848	>	Q_a = *(idat.quadrupole1);
849	>	trQa =  Q_a.trace();
850	>	Qar =   Q_a * rhat;
851	>	rQa = rhat * Q_a;
852	>	rdQar = dot(rhat, Qar);
853	>	rxQar = cross(rhat, Qar);
854	>	if (!idat.excluded)
855	>	Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or
856	>	+ rdQar * rhat * (dv22 - 2.0*v22or));
857	>	}
858
859	<	if (i_is_Charge) {
859	>	if (b_is_Charge) {
860	>	C_b = data2.fixedCharge;
861
862	<	if (j_is_Charge) {
863	<	if (screeningMethod_ == DAMPED) {
864	<	// assemble the damping variables
865	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
866	<	erfcVal = res.first;
867	<	derfcVal = res.second;
868	<	c1 = erfcVal * riji;
869	<	c2 = (-derfcVal + c1) * riji;
481	<	} else {
482	<	c1 = riji;
483	<	c2 = c1 * riji;
484	<	}
485	<
486	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
487	<
488	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
489	<	vterm = preVal * (c1 - c1c_);
490	<	dudr  = -idat.sw * preVal * c2;
491	<
492	<	} else if (summationMethod_ == SHIFTED_FORCE)  {
493	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
494	<	dudr  = idat.sw * preVal * (c2c_ - c2);
495	<
496	<	} else if (summationMethod_ == REACTION_FIELD) {
497	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
498	<	vterm = preVal * ( riji + rfVal );
499	<	dudr  = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
500	<
501	<	} else {
502	<	vterm = preVal * riji * erfcVal;
503	<
504	<	dudr  = - idat.sw * preVal * c2;
505	<
506	<	}
507	<
508	<	idat.vpair += vterm;
509	<	epot += idat.sw * vterm;
510	<
511	<	dVdr += dudr * rhat;
862	>	if (b_is_Fluctuating)
863	>	C_b += *(idat.flucQ2);
864	>
865	>	if (idat.excluded) {
866	>	*(idat.skippedCharge1) += C_b;
867	>	} else {
868	>	// only do the field if we're not excluded:
869	>	Ea += C_b *  pre11_ * dv01 * rhat;
870		}
871	<
514	<	if (j_is_Dipole) {
515	<	// pref is used by all the possible methods
516	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
517	<	preSw = idat.sw * pref;
518	<
519	<	if (summationMethod_ == REACTION_FIELD) {
520	<	ri2 = riji * riji;
521	<	ri3 = ri2 * riji;
871	>	}
872
873	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
874	<	idat.vpair += vterm;
875	<	epot += idat.sw * vterm;
873	>	if (b_is_Dipole) {
874	>	D_b = *(idat.dipole2);
875	>	rdDb = dot(rhat, D_b);
876	>	rxDb = cross(rhat, D_b);
877	>	if (!idat.excluded)
878	>	Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b);
879	>	}
880	>
881	>	if (b_is_Quadrupole) {
882	>	Q_b = *(idat.quadrupole2);
883	>	trQb =  Q_b.trace();
884	>	Qbr =   Q_b * rhat;
885	>	rQb = rhat * Q_b;
886	>	rdQbr = dot(rhat, Qbr);
887	>	rxQbr = cross(rhat, Qbr);
888	>	if (!idat.excluded)
889	>	Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or
890	>	+ rdQbr * rhat * (dv22 - 2.0*v22or));
891	>	}
892	>
893	>	if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) {
894	>	J = Jij[FQtids[idat.atid1]][FQtids[idat.atid2]];
895	>	}
896	>
897	>	if (a_is_Charge) {
898	>
899	>	if (b_is_Charge) {
900	>	pref =  pre11_ * *(idat.electroMult);
901	>	U  += C_a * C_b * pref * v01;
902	>	F  += C_a * C_b * pref * dv01 * rhat;
903	>
904	>	// If this is an excluded pair, there are still indirect
905	>	// interactions via the reaction field we must worry about:
906
907	<	dVdr +=  -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
908	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
907	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
908	>	rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2);
909	>	indirect_Pot += rfContrib;
910	>	indirect_F   += rfContrib * 2.0 * ri * rhat;
911	>	}
912	>
913	>	// Fluctuating charge forces are handled via Coulomb integrals
914	>	// for excluded pairs (i.e. those connected via bonds) and
915	>	// with the standard charge-charge interaction otherwise.
916
917	+	if (idat.excluded) {
918	+	if (a_is_Fluctuating || b_is_Fluctuating) {
919	+	coulInt = J->getValueAt( *(idat.rij) );
920	+	if (a_is_Fluctuating)  dUdCa += coulInt * C_b;
921	+	if (b_is_Fluctuating)  dUdCb += coulInt * C_a;
922	+	excluded_Pot += C_a * C_b * coulInt;
923	+	}
924		} else {
925	<	// determine the inverse r used if we have split dipoles
926	<	if (j_is_SplitDipole) {
927	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
928	<	ri = 1.0 / BigR;
535	<	scale = idat.rij * ri;
536	<	} else {
537	<	ri = riji;
538	<	scale = 1.0;
539	<	}
540	<
541	<	sc2 = scale * scale;
925	>	if (a_is_Fluctuating) dUdCa += C_b * pref * v01;
926	>	if (a_is_Fluctuating) dUdCb += C_a * pref * v01;
927	>	}
928	>	}
929
930	<	if (screeningMethod_ == DAMPED) {
931	<	// assemble the damping variables
932	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
933	<	erfcVal = res.first;
934	<	derfcVal = res.second;
548	<	c1 = erfcVal * ri;
549	<	c2 = (-derfcVal + c1) * ri;
550	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
551	<	} else {
552	<	c1 = ri;
553	<	c2 = c1 * ri;
554	<	c3 = 3.0 * c2 * ri;
555	<	}
556	<
557	<	c2ri = c2 * ri;
930	>	if (b_is_Dipole) {
931	>	pref =  pre12_ * *(idat.electroMult);
932	>	U  += C_a * pref * v11 * rdDb;
933	>	F  += C_a * pref * ((dv11 - v11or) * rdDb * rhat + v11or * D_b);
934	>	Tb += C_a * pref * v11 * rxDb;
935
936	<	// calculate the potential
560	<	pot_term =  scale * c2;
561	<	vterm = -pref * ct_j * pot_term;
562	<	idat.vpair += vterm;
563	<	epot += idat.sw * vterm;
564	<
565	<	// calculate derivatives for forces and torques
936	>	if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb;
937
938	<	dVdr += -preSw * (uz_j * c2ri - ct_j * rhat * sc2 * c3);
939	<	duduz_j += -preSw * pot_term * rhat;
938	>	// Even if we excluded this pair from direct interactions, we
939	>	// still have the reaction-field-mediated charge-dipole
940	>	// interaction:
941
942	+	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
943	+	rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij);
944	+	indirect_Pot += rfContrib * rdDb;
945	+	indirect_F   += rfContrib * D_b / (*idat.rij);
946	+	indirect_Tb  += C_a * pref * preRF_ * rxDb;
947		}
948		}
949
950	<	if (j_is_Quadrupole) {
951	<	// first precalculate some necessary variables
952	<	cx2 = cx_j * cx_j;
953	<	cy2 = cy_j * cy_j;
954	<	cz2 = cz_j * cz_j;
955	<	pref =  idat.electroMult * pre14_ * q_i * one_third_;
579	<
580	<	if (screeningMethod_ == DAMPED) {
581	<	// assemble the damping variables
582	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
583	<	erfcVal = res.first;
584	<	derfcVal = res.second;
585	<	c1 = erfcVal * riji;
586	<	c2 = (-derfcVal + c1) * riji;
587	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
588	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
589	<	} else {
590	<	c1 = riji;
591	<	c2 = c1 * riji;
592	<	c3 = 3.0 * c2 * riji;
593	<	c4 = 5.0 * c3 * riji * riji;
594	<	}
950	>	if (b_is_Quadrupole) {
951	>	pref = pre14_ * *(idat.electroMult);
952	>	U  +=  C_a * pref * (v21 * trQb + v22 * rdQbr);
953	>	F  +=  C_a * pref * (trQb * dv21 * rhat + 2.0 * Qbr * v22or);
954	>	F  +=  C_a * pref * rdQbr * rhat * (dv22 - 2.0*v22or);
955	>	Tb +=  C_a * pref * 2.0 * rxQbr * v22;
956
957	<	// precompute variables for convenience
597	<	preSw = idat.sw * pref;
598	<	c2ri = c2 * riji;
599	<	c3ri = c3 * riji;
600	<	c4rij = c4 * idat.rij;
601	<	rhatdot2 = 2.0 * rhat * c3;
602	<	rhatc4 = rhat * c4rij;
603	<
604	<	// calculate the potential
605	<	pot_term = ( qxx_j * (cx2*c3 - c2ri) +
606	<	qyy_j * (cy2*c3 - c2ri) +
607	<	qzz_j * (cz2*c3 - c2ri) );
608	<	vterm = pref * pot_term;
609	<	idat.vpair += vterm;
610	<	epot += idat.sw * vterm;
611	<
612	<	// calculate derivatives for the forces and torques
613	<
614	<	dVdr += -preSw * ( qxx_j* (cx2*rhatc4 - (2.0*cx_j*ux_j + rhat)*c3ri) +
615	<	qyy_j* (cy2*rhatc4 - (2.0*cy_j*uy_j + rhat)*c3ri) +
616	<	qzz_j* (cz2*rhatc4 - (2.0*cz_j*uz_j + rhat)*c3ri));
617	<
618	<	dudux_j += preSw * qxx_j * cx_j * rhatdot2;
619	<	duduy_j += preSw * qyy_j * cy_j * rhatdot2;
620	<	duduz_j += preSw * qzz_j * cz_j * rhatdot2;
957	>	if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr);
958		}
959		}
623	–
624	–	if (i_is_Dipole) {
960
961	<	if (j_is_Charge) {
627	<	// variables used by all the methods
628	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
629	<	preSw = idat.sw * pref;
961	>	if (a_is_Dipole) {
962
963	<	if (summationMethod_ == REACTION_FIELD) {
963	>	if (b_is_Charge) {
964	>	pref = pre12_ * *(idat.electroMult);
965
966	<	ri2 = riji * riji;
967	<	ri3 = ri2 * riji;
966	>	U  -= C_b * pref * v11 * rdDa;
967	>	F  -= C_b * pref * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
968	>	Ta -= C_b * pref * v11 * rxDa;
969
970	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
637	<	idat.vpair += vterm;
638	<	epot += idat.sw * vterm;
639	<
640	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
641	<
642	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
643	<
644	<	} else {
645	<
646	<	// determine inverse r if we are using split dipoles
647	<	if (i_is_SplitDipole) {
648	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
649	<	ri = 1.0 / BigR;
650	<	scale = idat.rij * ri;
651	<	} else {
652	<	ri = riji;
653	<	scale = 1.0;
654	<	}
655	<
656	<	sc2 = scale * scale;
657	<
658	<	if (screeningMethod_ == DAMPED) {
659	<	// assemble the damping variables
660	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
661	<	erfcVal = res.first;
662	<	derfcVal = res.second;
663	<	c1 = erfcVal * ri;
664	<	c2 = (-derfcVal + c1) * ri;
665	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
666	<	} else {
667	<	c1 = ri;
668	<	c2 = c1 * ri;
669	<	c3 = 3.0 * c2 * ri;
670	<	}
671	<
672	<	c2ri = c2 * ri;
673	<
674	<	// calculate the potential
675	<	pot_term = c2 * scale;
676	<	vterm = pref * ct_i * pot_term;
677	<	idat.vpair += vterm;
678	<	epot += idat.sw * vterm;
970	>	if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa;
971
972	<	// calculate derivatives for the forces and torques
973	<	dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
974	<	duduz_i += preSw * pot_term * rhat;
972	>	// Even if we excluded this pair from direct interactions,
973	>	// we still have the reaction-field-mediated charge-dipole
974	>	// interaction:
975	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
976	>	rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij);
977	>	indirect_Pot -= rfContrib * rdDa;
978	>	indirect_F   -= rfContrib * D_a / (*idat.rij);
979	>	indirect_Ta  -= C_b * pref * preRF_ * rxDa;
980		}
981		}
982
983	<	if (j_is_Dipole) {
984	<	// variables used by all methods
985	<	ct_ij = dot(uz_i, uz_j);
983	>	if (b_is_Dipole) {
984	>	pref = pre22_ * *(idat.electroMult);
985	>	DadDb = dot(D_a, D_b);
986	>	DaxDb = cross(D_a, D_b);
987
988	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
989	<	preSw = idat.sw * pref;
988	>	U  -= pref * (DadDb * v21 + rdDa * rdDb * v22);
989	>	F  -= pref * (dv21 * DadDb * rhat + v22or * (rdDb * D_a + rdDa * D_b));
990	>	F  -= pref * (rdDa * rdDb) * (dv22 - 2.0*v22or) * rhat;
991	>	Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa);
992	>	Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb);
993
994	<	if (summationMethod_ == REACTION_FIELD) {
995	<	ri2 = riji * riji;
996	<	ri3 = ri2 * riji;
997	<	ri4 = ri2 * ri2;
994	>	// Even if we excluded this pair from direct interactions, we
995	>	// still have the reaction-field-mediated dipole-dipole
996	>	// interaction:
997	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
998	>	rfContrib = -pref * preRF_ * 2.0;
999	>	indirect_Pot += rfContrib * DadDb;
1000	>	indirect_Ta  += rfContrib * DaxDb;
1001	>	indirect_Tb  -= rfContrib * DaxDb;
1002	>	}
1003	>	}
1004
1005	<	vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
1006	<	preRF2_ * ct_ij );
1007	<	idat.vpair += vterm;
1008	<	epot += idat.sw * vterm;
1009	<
703	<	a1 = 5.0 * ct_i * ct_j - ct_ij;
704	<
705	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
1005	>	if (b_is_Quadrupole) {
1006	>	pref = pre24_ * *(idat.electroMult);
1007	>	DadQb = D_a * Q_b;
1008	>	DadQbr = dot(D_a, Qbr);
1009	>	DaxQbr = cross(D_a, Qbr);
1010
1011	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
1012	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
1011	>	U  -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32);
1012	>	F  -= pref * (trQb*D_a + 2.0*DadQb) * v31or;
1013	>	F  -= pref * (trQb*rdDa + 2.0*DadQbr) * (dv31-v31or) * rhat;
1014	>	F  -= pref * (D_a*rdQbr + 2.0*rdDa*rQb) * v32or;
1015	>	F  -= pref * (rdDa * rdQbr * rhat * (dv32-3.0*v32or));
1016	>	Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32);
1017	>	Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31
1018	>	- 2.0*rdDa*rxQbr*v32);
1019	>	}
1020	>	}
1021
1022	<	} else {
1023	<
1024	<	if (i_is_SplitDipole) {
1025	<	if (j_is_SplitDipole) {
1026	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
1027	<	} else {
1028	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
717	<	}
718	<	ri = 1.0 / BigR;
719	<	scale = idat.rij * ri;
720	<	} else {
721	<	if (j_is_SplitDipole) {
722	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
723	<	ri = 1.0 / BigR;
724	<	scale = idat.rij * ri;
725	<	} else {
726	<	ri = riji;
727	<	scale = 1.0;
728	<	}
729	<	}
730	<	if (screeningMethod_ == DAMPED) {
731	<	// assemble damping variables
732	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
733	<	erfcVal = res.first;
734	<	derfcVal = res.second;
735	<	c1 = erfcVal * ri;
736	<	c2 = (-derfcVal + c1) * ri;
737	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
738	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * ri * ri;
739	<	} else {
740	<	c1 = ri;
741	<	c2 = c1 * ri;
742	<	c3 = 3.0 * c2 * ri;
743	<	c4 = 5.0 * c3 * ri * ri;
744	<	}
1022	>	if (a_is_Quadrupole) {
1023	>	if (b_is_Charge) {
1024	>	pref = pre14_ * *(idat.electroMult);
1025	>	U  += C_b * pref * (v21 * trQa + v22 * rdQar);
1026	>	F  += C_b * pref * (trQa * rhat * dv21 + 2.0 * Qar * v22or);
1027	>	F  += C_b * pref * rdQar * rhat * (dv22 - 2.0*v22or);
1028	>	Ta += C_b * pref * 2.0 * rxQar * v22;
1029
1030	<	// precompute variables for convenience
1031	<	sc2 = scale * scale;
1032	<	cti3 = ct_i * sc2 * c3;
1033	<	ctj3 = ct_j * sc2 * c3;
1034	<	ctidotj = ct_i * ct_j * sc2;
1035	<	preSwSc = preSw * scale;
1036	<	c2ri = c2 * ri;
753	<	c3ri = c3 * ri;
754	<	c4rij = c4 * idat.rij;
1030	>	if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar);
1031	>	}
1032	>	if (b_is_Dipole) {
1033	>	pref = pre24_ * *(idat.electroMult);
1034	>	DbdQa = D_b * Q_a;
1035	>	DbdQar = dot(D_b, Qar);
1036	>	DbxQar = cross(D_b, Qar);
1037
1038	<	// calculate the potential
1039	<	pot_term = (ct_ij * c2ri - ctidotj * c3);
1040	<	vterm = pref * pot_term;
1041	<	idat.vpair += vterm;
1042	<	epot += idat.sw * vterm;
1043	<
1044	<	// calculate derivatives for the forces and torques
1045	<	dVdr += preSwSc * ( ctidotj * rhat * c4rij  -
764	<	(ct_i*uz_j + ct_j*uz_i + ct_ij*rhat) * c3ri);
765	<
766	<	duduz_i += preSw * (uz_j * c2ri - ctj3 * rhat);
767	<	duduz_j += preSw * (uz_i * c2ri - cti3 * rhat);
768	<	}
1038	>	U  += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32);
1039	>	F  += pref * (trQa*D_b + 2.0*DbdQa) * v31or;
1040	>	F  += pref * (trQa*rdDb + 2.0*DbdQar) * (dv31-v31or) * rhat;
1041	>	F  += pref * (D_b*rdQar + 2.0*rdDb*rQa) * v32or;
1042	>	F  += pref * (rdDb * rdQar * rhat * (dv32-3.0*v32or));
1043	>	Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31
1044	>	+ 2.0*rdDb*rxQar*v32);
1045	>	Tb += pref * ((trQa*rxDb - 2.0 * DbxQar)*v31 + rxDb*rdQar*v32);
1046		}
1047	<	}
1047	>	if (b_is_Quadrupole) {
1048	>	pref = pre44_ * *(idat.electroMult);  // yes
1049	>	QaQb = Q_a * Q_b;
1050	>	trQaQb = QaQb.trace();
1051	>	rQaQb = rhat * QaQb;
1052	>	QaQbr = QaQb * rhat;
1053	>	QaxQb = cross(Q_a, Q_b);
1054	>	rQaQbr = dot(rQa, Qbr);
1055	>	rQaxQbr = cross(rQa, Qbr);
1056	>
1057	>	U  += pref * (trQa * trQb + 2.0 * trQaQb) * v41;
1058	>	U  += pref * (trQa * rdQbr + trQb * rdQar  + 4.0 * rQaQbr) * v42;
1059	>	U  += pref * (rdQar * rdQbr) * v43;
1060
1061	<	if (i_is_Quadrupole) {
1062	<	if (j_is_Charge) {
1063	<	// precompute some necessary variables
775	<	cx2 = cx_i * cx_i;
776	<	cy2 = cy_i * cy_i;
777	<	cz2 = cz_i * cz_i;
1061	>	F  += pref * rhat * (trQa * trQb + 2.0 * trQaQb)*dv41;
1062	>	F  += pref*rhat*(trQa*rdQbr + trQb*rdQar + 4.0*rQaQbr)*(dv42-2.0*v42or);
1063	>	F  += pref * rhat * (rdQar * rdQbr)*(dv43 - 4.0*v43or);
1064
1065	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
1065	>	F  += pref * 2.0 * (trQb*rQa + trQa*rQb) * v42or;
1066	>	F  += pref * 4.0 * (rQaQb + QaQbr) * v42or;
1067	>	F  += pref * 2.0 * (rQa*rdQbr + rdQar*rQb) * v43or;
1068
1069	<	if (screeningMethod_ == DAMPED) {
1070	<	// assemble the damping variables
1071	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
1072	<	erfcVal = res.first;
1073	<	derfcVal = res.second;
786	<	c1 = erfcVal * riji;
787	<	c2 = (-derfcVal + c1) * riji;
788	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
789	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
790	<	} else {
791	<	c1 = riji;
792	<	c2 = c1 * riji;
793	<	c3 = 3.0 * c2 * riji;
794	<	c4 = 5.0 * c3 * riji * riji;
795	<	}
796	<
797	<	// precompute some variables for convenience
798	<	preSw = idat.sw * pref;
799	<	c2ri = c2 * riji;
800	<	c3ri = c3 * riji;
801	<	c4rij = c4 * idat.rij;
802	<	rhatdot2 = 2.0 * rhat * c3;
803	<	rhatc4 = rhat * c4rij;
1069	>	Ta += pref * (- 4.0 * QaxQb * v41);
1070	>	Ta += pref * (- 2.0 * trQb * cross(rQa, rhat)
1071	>	+ 4.0 * cross(rhat, QaQbr)
1072	>	- 4.0 * rQaxQbr) * v42;
1073	>	Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43;
1074
805	–	// calculate the potential
806	–	pot_term = ( qxx_i * (cx2 * c3 - c2ri) +
807	–	qyy_i * (cy2 * c3 - c2ri) +
808	–	qzz_i * (cz2 * c3 - c2ri) );
809	–
810	–	vterm = pref * pot_term;
811	–	idat.vpair += vterm;
812	–	epot += idat.sw * vterm;
1075
1076	<	// calculate the derivatives for the forces and torques
1076	>	Tb += pref * (+ 4.0 * QaxQb * v41);
1077	>	Tb += pref * (- 2.0 * trQa * cross(rQb, rhat)
1078	>	- 4.0 * cross(rQaQb, rhat)
1079	>	+ 4.0 * rQaxQbr) * v42;
1080	>	// Possible replacement for line 2 above:
1081	>	//             + 4.0 * cross(rhat, QbQar)
1082
1083	<	dVdr += -preSw * (qxx_i* (cx2*rhatc4 - (2.0*cx_i*ux_i + rhat)*c3ri) +
817	<	qyy_i* (cy2*rhatc4 - (2.0*cy_i*uy_i + rhat)*c3ri) +
818	<	qzz_i* (cz2*rhatc4 - (2.0*cz_i*uz_i + rhat)*c3ri));
1083	>	Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43;
1084
820	–	dudux_i += preSw * qxx_i * cx_i *  rhatdot2;
821	–	duduy_i += preSw * qyy_i * cy_i *  rhatdot2;
822	–	duduz_i += preSw * qzz_i * cz_i *  rhatdot2;
1085		}
1086		}
1087
1088	<	idat.pot += epot;
1089	<	idat.f1 += dVdr;
1090	<
829	<	if (i_is_Dipole || i_is_Quadrupole)
830	<	idat.t1 -= cross(uz_i, duduz_i);
831	<	if (i_is_Quadrupole) {
832	<	idat.t1 -= cross(ux_i, dudux_i);
833	<	idat.t1 -= cross(uy_i, duduy_i);
1088	>	if (idat.doElectricField) {
1089	>	*(idat.eField1) += Ea * *(idat.electroMult);
1090	>	*(idat.eField2) += Eb * *(idat.electroMult);
1091		}
1092
1093	<	if (j_is_Dipole || j_is_Quadrupole)
1094	<	idat.t2 -= cross(uz_j, duduz_j);
838	<	if (j_is_Quadrupole) {
839	<	idat.t2 -= cross(uz_j, dudux_j);
840	<	idat.t2 -= cross(uz_j, duduy_j);
841	<	}
1093	>	if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1094	>	if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1095
1096	<	return;
1097	<	}
1096	>	if (!idat.excluded) {
1097	>
1098	>	*(idat.vpair) += U;
1099	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw);
1100	>	*(idat.f1) += F * *(idat.sw);
1101	>
1102	>	if (a_is_Dipole || a_is_Quadrupole)
1103	>	*(idat.t1) += Ta * *(idat.sw);
1104
1105	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
1105	>	if (b_is_Dipole || b_is_Quadrupole)
1106	>	*(idat.t2) += Tb * *(idat.sw);
1107	>
1108	>	} else {
1109	>
1110	>	// only accumulate the forces and torques resulting from the
1111	>	// indirect reaction field terms.
1112
1113	<	if (!initialized_) initialize();
1113	>	*(idat.vpair) += indirect_Pot;
1114	>	(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] +=  excluded_Pot;
1115	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot;
1116	>	*(idat.f1) += *(idat.sw) * indirect_F;
1117	>
1118	>	if (a_is_Dipole || a_is_Quadrupole)
1119	>	*(idat.t1) += *(idat.sw) * indirect_Ta;
1120	>
1121	>	if (b_is_Dipole || b_is_Quadrupole)
1122	>	*(idat.t2) += *(idat.sw) * indirect_Tb;
1123	>	}
1124	>	return;
1125	>	}
1126
1127	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
851	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
852	<
853	<	// logicals
1127	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1128
1129	<	bool i_is_Charge = data1.is_Charge;
856	<	bool i_is_Dipole = data1.is_Dipole;
1129	>	if (!initialized_) initialize();
1130
1131	<	bool j_is_Charge = data2.is_Charge;
859	<	bool j_is_Dipole = data2.is_Dipole;
860	<
861	<	RealType q_i, q_j;
1131	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[sdat.atid]];
1132
1133	<	// The skippedCharge computation is needed by the real-space cutoff methods
1134	<	// (i.e. shifted force and shifted potential)
1133	>	// logicals
1134	>	bool i_is_Charge = data.is_Charge;
1135	>	bool i_is_Dipole = data.is_Dipole;
1136	>	bool i_is_Quadrupole = data.is_Quadrupole;
1137	>	bool i_is_Fluctuating = data.is_Fluctuating;
1138	>	RealType C_a = data.fixedCharge;
1139	>	RealType self(0.0), preVal, DdD, trQ, trQQ;
1140
1141	<	if (i_is_Charge) {
1142	<	q_i = data1.charge;
868	<	skdat.skippedCharge2 += q_i;
1141	>	if (i_is_Dipole) {
1142	>	DdD = data.dipole.lengthSquare();
1143		}
1144	<
1145	<	if (j_is_Charge) {
1146	<	q_j = data2.charge;
1147	<	skdat.skippedCharge1 += q_j;
1144	>
1145	>	if (i_is_Fluctuating) {
1146	>	C_a += *(sdat.flucQ);
1147	>	// dVdFQ is really a force, so this is negative the derivative
1148	>	*(sdat.dVdFQ) -=  *(sdat.flucQ) * data.hardness + data.electronegativity;
1149	>	(*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) *
1150	>	(*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity);
1151		}
1152
1153	<	// the rest of this function should only be necessary for reaction field.
1154	<
878	<	if (summationMethod_ == REACTION_FIELD) {
879	<	RealType riji, ri2, ri3;
880	<	RealType q_i, mu_i, ct_i;
881	<	RealType q_j, mu_j, ct_j;
882	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
883	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
884	<
885	<	// some variables we'll need independent of electrostatic type:
1153	>	switch (summationMethod_) {
1154	>	case esm_REACTION_FIELD:
1155
887	–	riji = 1.0 / skdat.rij;
888	–	rhat = skdat.d  * riji;
889	–
890	–	if (i_is_Dipole) {
891	–	mu_i = data1.dipole_moment;
892	–	uz_i = skdat.eFrame1.getColumn(2);
893	–	ct_i = dot(uz_i, rhat);
894	–	duduz_i = V3Zero;
895	–	}
896	–
897	–	if (j_is_Dipole) {
898	–	mu_j = data2.dipole_moment;
899	–	uz_j = skdat.eFrame2.getColumn(2);
900	–	ct_j = dot(uz_j, rhat);
901	–	duduz_j = V3Zero;
902	–	}
903	–
1156		if (i_is_Charge) {
1157	<	if (j_is_Charge) {
1158	<	preVal = skdat.electroMult * pre11_ * q_i * q_j;
1159	<	rfVal = preRF_ * skdat.rij * skdat.rij;
1160	<	vterm = preVal * rfVal;
1161	<	myPot += skdat.sw * vterm;
910	<	dudr  = skdat.sw * preVal * 2.0 * rfVal * riji;
911	<	dVdr += dudr * rhat;
912	<	}
913	<
914	<	if (j_is_Dipole) {
915	<	ri2 = riji * riji;
916	<	ri3 = ri2 * riji;
917	<	pref = skdat.electroMult * pre12_ * q_i * mu_j;
918	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
919	<	myPot += skdat.sw * vterm;
920	<	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
921	<	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
922	<	}
1157	>	// Self potential [see Wang and Hermans, "Reaction Field
1158	>	// Molecular Dynamics Simulation with Friedman’s Image Charge
1159	>	// Method," J. Phys. Chem. 99, 12001-12007 (1995).]
1160	>	preVal = pre11_ * preRF_ * C_a * C_a;
1161	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 * preVal / cutoffRadius_;
1162		}
1163	+
1164		if (i_is_Dipole) {
1165	<	if (j_is_Charge) {
926	<	ri2 = riji * riji;
927	<	ri3 = ri2 * riji;
928	<	pref = skdat.electroMult * pre12_ * q_j * mu_i;
929	<	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
930	<	myPot += skdat.sw * vterm;
931	<	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
932	<	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
933	<	}
1165	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DdD;
1166		}
1167
1168	<	// accumulate the forces and torques resulting from the self term
937	<	skdat.pot += myPot;
938	<	skdat.f1 += dVdr;
1168	>	break;
1169
1170	+	case esm_SHIFTED_FORCE:
1171	+	case esm_SHIFTED_POTENTIAL:
1172	+	case esm_TAYLOR_SHIFTED:
1173	+	case esm_EWALD_FULL:
1174	+	if (i_is_Charge)
1175	+	self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge));
1176		if (i_is_Dipole)
1177	<	skdat.t1 -= cross(uz_i, duduz_i);
1178	<	if (j_is_Dipole)
1179	<	skdat.t2 -= cross(uz_j, duduz_j);
1177	>	self += selfMult2_ * pre22_ * DdD;
1178	>	if (i_is_Quadrupole) {
1179	>	trQ = data.quadrupole.trace();
1180	>	trQQ = (data.quadrupole * data.quadrupole).trace();
1181	>	self += selfMult4_ * pre44_ * (2.0*trQQ + trQ*trQ);
1182	>	if (i_is_Charge)
1183	>	self -= selfMult2_ * pre14_ * 2.0 * C_a * trQ;
1184	>	}
1185	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1186	>	break;
1187	>	default:
1188	>	break;
1189		}
1190		}
1191	+
1192	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
1193	+	// This seems to work moderately well as a default.  There's no
1194	+	// inherent scale for 1/r interactions that we can standardize.
1195	+	// 12 angstroms seems to be a reasonably good guess for most
1196	+	// cases.
1197	+	return 12.0;
1198	+	}
1199	+
1200	+
1201	+	void Electrostatic::ReciprocalSpaceSum(potVec& pot) {
1202
1203	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1204	<	RealType mu1, preVal, chg1, self;
1203	>	RealType kPot = 0.0;
1204	>	RealType kVir = 0.0;
1205
1206	<	if (!initialized_) initialize();
1206	>	const RealType mPoleConverter = 0.20819434; // converts from the
1207	>	// internal units of
1208	>	// Debye (for dipoles)
1209	>	// or Debye-angstroms
1210	>	// (for quadrupoles) to
1211	>	// electron angstroms or
1212	>	// electron-angstroms^2
1213
1214	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1215	<
1216	<	// logicals
1214	>	const RealType eConverter = 332.0637778; // convert the
1215	>	// Charge-Charge
1216	>	// electrostatic
1217	>	// interactions into kcal /
1218	>	// mol assuming distances
1219	>	// are measured in
1220	>	// angstroms.
1221
1222	<	bool i_is_Charge = data.is_Charge;
1223	<	bool i_is_Dipole = data.is_Dipole;
1224	<
1225	<	if (summationMethod_ == REACTION_FIELD) {
1226	<	if (i_is_Dipole) {
1227	<	mu1 = data.dipole_moment;
1228	<	preVal = pre22_ * preRF2_ * mu1 * mu1;
1229	<	scdat.pot -= 0.5 * preVal;
1222	>	Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
1223	>	Vector3d box = hmat.diagonals();
1224	>	RealType boxMax = box.max();
1225	>
1226	>	cerr << "da = " << dampingAlpha_ << " rc = " << cutoffRadius_ << "\n";
1227	>	cerr << "boxMax = " << boxMax << "\n";
1228	>	//int kMax = int(2.0 * M_PI / (pow(dampingAlpha_,2)*cutoffRadius_ * boxMax) );
1229	>	int kMax = 5;
1230	>	cerr << "kMax = " << kMax << "\n";
1231	>	int kSqMax = kMax*kMax + 2;
1232	>
1233	>	int kLimit = kMax+1;
1234	>	int kLim2 = 2*kMax+1;
1235	>	int kSqLim = kSqMax;
1236	>
1237	>	vector<RealType> AK(kSqLim+1, 0.0);
1238	>	RealType xcl = 2.0 * M_PI / box.x();
1239	>	RealType ycl = 2.0 * M_PI / box.y();
1240	>	RealType zcl = 2.0 * M_PI / box.z();
1241	>	RealType rcl = 2.0 * M_PI / boxMax;
1242	>	RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z());
1243	>
1244	>	if(dampingAlpha_ < 1.0e-12) return;
1245	>
1246	>	RealType ralph = -0.25/pow(dampingAlpha_,2);
1247	>
1248	>	// Calculate and store exponential factors
1249	>
1250	>	vector<vector<Vector3d> > eCos;
1251	>	vector<vector<Vector3d> > eSin;
1252	>
1253	>	int nMax = info_->getNAtoms();
1254	>
1255	>	eCos.resize(kLimit+1);
1256	>	eSin.resize(kLimit+1);
1257	>	for (int j = 0; j < kLimit+1; j++) {
1258	>	eCos[j].resize(nMax);
1259	>	eSin[j].resize(nMax);
1260	>	}
1261	>
1262	>	Vector3d t( 2.0 * M_PI );
1263	>	t.Vdiv(t, box);
1264	>
1265	>	SimInfo::MoleculeIterator mi;
1266	>	Molecule::AtomIterator ai;
1267	>	int i;
1268	>	Vector3d r;
1269	>	Vector3d tt;
1270	>	Vector3d w;
1271	>	Vector3d u;
1272	>	Vector3d a;
1273	>	Vector3d b;
1274	>
1275	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1276	>	mol = info_->nextMolecule(mi)) {
1277	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1278	>	atom = mol->nextAtom(ai)) {
1279
1280	<	// The self-correction term adds into the reaction field vector
1281	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1282	<	Vector3d ei = preVal * uz_i;
1280	>	i = atom->getLocalIndex();
1281	>	r = atom->getPos();
1282	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r);
1283	>
1284	>	// Shift so that all coordinates are in the range [0,L]:
1285
1286	<	// This looks very wrong.  A vector crossed with itself is zero.
1287	<	scdat.t -= cross(uz_i, ei);
1286	>	r += box/2.0;
1287	>
1288	>	tt.Vmul(t, r);
1289	>
1290	>	//cerr << "tt = " << tt << "\n";
1291	>
1292	>	eCos[1][i] = Vector3d(1.0, 1.0, 1.0);
1293	>	eSin[1][i] = Vector3d(0.0, 0.0, 0.0);
1294	>	eCos[2][i] = Vector3d(cos(tt.x()), cos(tt.y()), cos(tt.z()));
1295	>	eSin[2][i] = Vector3d(sin(tt.x()), sin(tt.y()), sin(tt.z()));
1296	>	u = eCos[2][i];
1297	>	w = eSin[2][i];
1298	>
1299	>	for(int l = 3; l <= kLimit; l++) {
1300	>	a.Vmul(eCos[l-1][i], u);
1301	>	b.Vmul(eSin[l-1][i], w);
1302	>	eCos[l][i] = a - b;
1303	>	a.Vmul(eSin[l-1][i], u);
1304	>	b.Vmul(eCos[l-1][i], w);
1305	>	eSin[l][i] = a + b;
1306	>	}
1307		}
1308	<	} else if (summationMethod_ == SHIFTED_FORCE || summationMethod_ == SHIFTED_POTENTIAL) {
1309	<	if (i_is_Charge) {
1310	<	chg1 = data.charge;
1311	<	if (screeningMethod_ == DAMPED) {
1312	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1313	<	} else {
1314	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1308	>	}
1309	>
1310	>	// Calculate and store AK coefficients:
1311	>
1312	>	RealType eksq = 1.0;
1313	>	RealType expf = 0.0;
1314	>	if (ralph < 0.0) expf = exp(ralph*rcl*rcl);
1315	>	for (i = 1; i <= kSqLim; i++) {
1316	>	RealType rksq = float(i)*rcl*rcl;
1317	>	eksq = expf*eksq;
1318	>	AK[i] = eConverter * eksq/rksq;
1319	>	}
1320	>
1321	>	/*
1322	>	* Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz)
1323	>	* the values of ll, mm and nn are selected so that the symmetry of
1324	>	* reciprocal lattice is taken into account i.e. the following
1325	>	* rules apply.
1326	>	*
1327	>	* ll ranges over the values 0 to kMax only.
1328	>	*
1329	>	* mm ranges over 0 to kMax when ll=0 and over
1330	>	*            -kMax to kMax otherwise.
1331	>	* nn ranges over 1 to kMax when ll=mm=0 and over
1332	>	*            -kMax to kMax otherwise.
1333	>	*
1334	>	* Hence the result of the summation must be doubled at the end.
1335	>	*/
1336	>
1337	>	std::vector<RealType> clm(nMax, 0.0);
1338	>	std::vector<RealType> slm(nMax, 0.0);
1339	>	std::vector<RealType> ckr(nMax, 0.0);
1340	>	std::vector<RealType> skr(nMax, 0.0);
1341	>	std::vector<RealType> ckc(nMax, 0.0);
1342	>	std::vector<RealType> cks(nMax, 0.0);
1343	>	std::vector<RealType> dkc(nMax, 0.0);
1344	>	std::vector<RealType> dks(nMax, 0.0);
1345	>	std::vector<RealType> qkc(nMax, 0.0);
1346	>	std::vector<RealType> qks(nMax, 0.0);
1347	>	std::vector<Vector3d> dxk(nMax, V3Zero);
1348	>	std::vector<Vector3d> qxk(nMax, V3Zero);
1349	>
1350	>	int mMin = kLimit;
1351	>	int nMin = kLimit + 1;
1352	>	for (int l = 1; l <= kLimit; l++) {
1353	>	int ll =l - 1;
1354	>	RealType rl = xcl * float(ll);
1355	>	for (int mmm = mMin; mmm <= kLim2; mmm++) {
1356	>	int mm = mmm - kLimit;
1357	>	int m = abs(mm) + 1;
1358	>	RealType rm = ycl * float(mm);
1359	>	// Set temporary products of exponential terms
1360	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1361	>	mol = info_->nextMolecule(mi)) {
1362	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1363	>	atom = mol->nextAtom(ai)) {
1364	>
1365	>	i = atom->getLocalIndex();
1366	>	if(mm < 0) {
1367	>	clm[i] = eCos[l][i].x()*eCos[m][i].y()
1368	>	+ eSin[l][i].x()*eSin[m][i].y();
1369	>	slm[i] = eSin[l][i].x()*eCos[m][i].y()
1370	>	- eSin[m][i].y()*eCos[l][i].x();
1371	>	} else {
1372	>	clm[i] = eCos[l][i].x()*eCos[m][i].y()
1373	>	- eSin[l][i].x()*eSin[m][i].y();
1374	>	slm[i] = eSin[l][i].x()*eCos[m][i].y()
1375	>	+ eSin[m][i].y()*eCos[l][i].x();
1376	>	}
1377	>	}
1378		}
1379	<	scdat.pot += self;
1379	>	for (int nnn = nMin; nnn <= kLim2; nnn++) {
1380	>	int nn = nnn - kLimit;
1381	>	int n = abs(nn) + 1;
1382	>	RealType rn = zcl * float(nn);
1383	>	// Test on magnitude of k vector:
1384	>	int kk=ll*ll + mm*mm + nn*nn;
1385	>	if(kk <= kSqLim) {
1386	>	Vector3d kVec = Vector3d(rl, rm, rn);
1387	>	Mat3x3d  k2 = outProduct(kVec, kVec);
1388	>	// Calculate exp(ikr) terms
1389	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1390	>	mol = info_->nextMolecule(mi)) {
1391	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1392	>	atom = mol->nextAtom(ai)) {
1393	>	i = atom->getLocalIndex();
1394	>
1395	>	if (nn < 0) {
1396	>	ckr[i]=clm[i]*eCos[n][i].z()+slm[i]*eSin[n][i].z();
1397	>	skr[i]=slm[i]*eCos[n][i].z()-clm[i]*eSin[n][i].z();
1398	>	} else {
1399	>	ckr[i]=clm[i]*eCos[n][i].z()-slm[i]*eSin[n][i].z();
1400	>	skr[i]=slm[i]*eCos[n][i].z()+clm[i]*eSin[n][i].z();
1401	>	}
1402	>	}
1403	>	}
1404	>
1405	>	// Calculate scalar and vector products for each site:
1406	>
1407	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1408	>	mol = info_->nextMolecule(mi)) {
1409	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1410	>	atom = mol->nextAtom(ai)) {
1411	>	i = atom->getLocalIndex();
1412	>	int atid = atom->getAtomType()->getIdent();
1413	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]];
1414	>
1415	>	if (data.is_Charge) {
1416	>	RealType C = data.fixedCharge;
1417	>	if (atom->isFluctuatingCharge()) C += atom->getFlucQPos();
1418	>	ckc[i] = C * ckr[i];
1419	>	cks[i] = C * skr[i];
1420	>	}
1421	>
1422	>	if (data.is_Dipole) {
1423	>	Vector3d D = atom->getDipole() * mPoleConverter;
1424	>	RealType dk = dot(kVec, D);
1425	>	dxk[i] = cross(kVec, D);
1426	>	dkc[i] = dk * ckr[i];
1427	>	dks[i] = dk * skr[i];
1428	>	}
1429	>	if (data.is_Quadrupole) {
1430	>	Mat3x3d Q = atom->getQuadrupole();
1431	>	Q *= mPoleConverter;
1432	>	RealType qk = -( Q * k2 ).trace();
1433	>	qxk[i] = -2.0 * cross(k2, Q);
1434	>	qkc[i] = qk * ckr[i];
1435	>	qks[i] = qk * skr[i];
1436	>	}
1437	>	}
1438	>	}
1439	>
1440	>	// calculate vector sums
1441	>
1442	>	RealType ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0);
1443	>	RealType ckss = std::accumulate(cks.begin(),cks.end(),0.0);
1444	>	RealType dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0);
1445	>	RealType dkss = std::accumulate(dks.begin(),dks.end(),0.0);
1446	>	RealType qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0);
1447	>	RealType qkss = std::accumulate(qks.begin(),qks.end(),0.0);
1448	>
1449	>
1450	>	#ifdef IS_MPI
1451	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckcs, 1, MPI::REALTYPE,
1452	>	MPI::SUM);
1453	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckss, 1, MPI::REALTYPE,
1454	>	MPI::SUM);
1455	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkcs, 1, MPI::REALTYPE,
1456	>	MPI::SUM);
1457	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkss, 1, MPI::REALTYPE,
1458	>	MPI::SUM);
1459	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkcs, 1, MPI::REALTYPE,
1460	>	MPI::SUM);
1461	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkss, 1, MPI::REALTYPE,
1462	>	MPI::SUM);
1463	>	#endif
1464	>
1465	>	// Accumulate potential energy and virial contribution:
1466	>
1467	>	kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss)
1468	>	+ (ckcs-dkss-qkcs)*(ckcs-dkss-qkss));
1469	>
1470	>	kVir -= 2.0 * rvol * AK[kk]*(ckcs*ckcs+ckss*ckss
1471	>	+4.0*(ckss*dkcs-ckcs*dkss)
1472	>	+3.0*(dkcs*dkcs+dkss*dkss)
1473	>	-6.0*(ckss*qkss+ckcs*qkcs)
1474	>	+8.0*(dkss*qkcs-dkcs*qkss)
1475	>	+5.0*(qkss*qkss+qkcs*qkcs));
1476	>
1477	>	// Calculate force and torque for each site:
1478	>
1479	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1480	>	mol = info_->nextMolecule(mi)) {
1481	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1482	>	atom = mol->nextAtom(ai)) {
1483	>
1484	>	i = atom->getLocalIndex();
1485	>	int atid = atom->getAtomType()->getIdent();
1486	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]];
1487	>
1488	>	RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs)
1489	>	- (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss));
1490	>	RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs)
1491	>	-ckr[i]*(ckss+dkcs-qkss));
1492	>	RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)+
1493	>	skr[i]*(ckss+dkcs-qkss));
1494	>
1495	>
1496	>	atom->addFrc( 4.0 * rvol * qfrc * kVec );
1497	>
1498	>	if (data.is_Dipole) {
1499	>	atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] );
1500	>	}
1501	>	if (data.is_Quadrupole) {
1502	>	atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] );
1503	>	}
1504	>	}
1505	>	}
1506	>	}
1507	>	}
1508		}
1509		}
1510	+	cerr << "kPot = " << kPot << "\n";
1511	+	pot[ELECTROSTATIC_FAMILY] += kPot;
1512		}
984	–
985	–	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
986	–	// This seems to work moderately well as a default.  There's no
987	–	// inherent scale for 1/r interactions that we can standardize.
988	–	// 12 angstroms seems to be a reasonably good guess for most
989	–	// cases.
990	–	return 12.0;
991	–	}
1513		}

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