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

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branches/development/src/nonbonded/Electrostatic.cpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
trunk/src/nonbonded/Electrostatic.cpp (file contents), Revision 1915 by gezelter, Mon Jul 29 17:55:17 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		#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), info_(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;
#	Line 74 | 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
#	Line 94 | Line 118 | namespace OpenMD {
118		summationMethod_ = esm_HARD;
119		screeningMethod_ = UNDAMPED;
120		dielectric_ = 1.0;
97	–	one_third_ = 1.0 / 3.0;
98	–	haveCutoffRadius_ = false;
99	–	haveDampingAlpha_ = false;
100	–	haveDielectric_ = false;
101	–	haveElectroSpline_ = false;
121
122		// check the summation method:
123		if (simParams_->haveElectrostaticSummationMethod()) {
#	Line 111 | Line 130 | namespace OpenMD {
130		} else {
131		// throw error
132		sprintf( painCave.errMsg,
133	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
133	>	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
134		"\t(Input file specified %s .)\n"
135	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
136	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
137	<	"\t\"reaction_field\".\n", myMethod.c_str() );
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		}
#	Line 174 | Line 194 | namespace OpenMD {
194		simError();
195		}
196
197	<	if (screeningMethod_ == DAMPED) {
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;
183	<
202	>	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
203		// throw warning
204		sprintf( painCave.errMsg,
205	<	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
206	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
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;
#	Line 195 | Line 215 | namespace OpenMD {
215		haveDampingAlpha_ = true;
216		}
217
198	–	// find all of the Electrostatic atom Types:
199	–	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
200	–	ForceField::AtomTypeContainer::MapTypeIterator i;
201	–	AtomType* at;
202	–
203	–	for (at = atomTypes->beginType(i); at != NULL;
204	–	at = atomTypes->nextType(i)) {
205	–
206	–	if (at->isElectrostatic())
207	–	addType(at);
208	–	}
209	–
218
219	<	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
220	<	rcuti_ = 1.0 / cutoffRadius_;
221	<	rcuti2_ = rcuti_ * rcuti_;
222	<	rcuti3_ = rcuti2_ * rcuti_;
223	<	rcuti4_ = rcuti2_ * 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	<	if (screeningMethod_ == DAMPED) {
229	<
219	<	alpha2_ = dampingAlpha_ * dampingAlpha_;
220	<	alpha4_ = alpha2_ * alpha2_;
221	<	alpha6_ = alpha4_ * alpha2_;
222	<	alpha8_ = alpha4_ * alpha4_;
223	<
224	<	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
225	<	invRootPi_ = 0.56418958354775628695;
226	<	alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
228	>	Etids.resize( forceField_->getNAtomType(), -1);
229	>	FQtids.resize( forceField_->getNAtomType(), -1);
230
231	<	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
232	<	c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
233	<	c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
234	<	c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
232	<	c5c_ = 8.0 * alphaPi_ * alpha6_ + 7.0 * c4c_ * rcuti2_;
233	<	c6c_ = 16.0 * alphaPi_ * alpha8_ + 9.0 * c5c_ * rcuti2_;
234	<	} else {
235	<	c1c_ = rcuti_;
236	<	c2c_ = c1c_ * rcuti_;
237	<	c3c_ = 3.0 * c2c_ * rcuti_;
238	<	c4c_ = 5.0 * c3c_ * rcuti2_;
239	<	c5c_ = 7.0 * c4c_ * rcuti2_;
240	<	c6c_ = 9.0 * c5c_ * rcuti2_;
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	<
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) * cutoffRadius2_ * cutoffRadius_);
246	<	preRF2_ = 2.0 * preRF_;
245	>	((2.0 * dielectric_ + 1.0) * pow(cutoffRadius_,3) );
246		}
247
248	<	RealType dx = cutoffRadius_ / RealType(np_ - 1);
249	<	RealType rval;
250	<	vector<RealType> rvals;
251	<	vector<RealType> yvals;
252	<	for (int i = 0; i < np_; i++) {
253	<	rval = RealType(i) * dx;
254	<	rvals.push_back(rval);
255	<	yvals.push_back(erfc(dampingAlpha_ * rval));
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	>	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		}
258	–	erfcSpline_ = new CubicSpline();
259	–	erfcSpline_->addPoints(rvals, yvals);
260	–	haveElectroSpline_ = true;
284
285	<	initialized_ = true;
286	<	}
287	<
288	<	void Electrostatic::addType(AtomType* atomType){
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	<	ElectrostaticAtomData electrostaticAtomData;
293	<	electrostaticAtomData.is_Charge = false;
294	<	electrostaticAtomData.is_Dipole = false;
295	<	electrostaticAtomData.is_SplitDipole = false;
296	<	electrostaticAtomData.is_Quadrupole = false;
292	>	if (summationMethod_ != esm_EWALD_FULL) {
293	>	selfMult1_ -= b0c;
294	>	selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
295	>	selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
296	>	}
297
298	<	if (atomType->isCharge()) {
299	<	GenericData* data = atomType->getPropertyByName("Charge");
298	>	// working variables for the splines:
299	>	RealType ri, ri2;
300	>	RealType b0, b1, b2, b3, b4, b5;
301	>	RealType db0_1, db0_2, db0_3, db0_4, db0_5;
302	>	RealType f, fc, f0;
303	>	RealType g, gc, g0, g1, g2, g3, g4;
304	>	RealType h, hc, h1, h2, h3, h4;
305	>	RealType s, sc, s2, s3, s4;
306	>	RealType t, tc, t3, t4;
307	>	RealType u, uc, u4;
308
309	<	if (data == NULL) {
310	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
278	<	"Charge\n"
279	<	"\tparameters for atomType %s.\n",
280	<	atomType->getName().c_str());
281	<	painCave.severity = OPENMD_ERROR;
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
286	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
287	<	if (doubleData == NULL) {
288	<	sprintf( painCave.errMsg,
289	<	"Electrostatic::addType could not convert GenericData to "
290	<	"Charge for\n"
291	<	"\tatom type %s\n", atomType->getName().c_str());
292	<	painCave.severity = OPENMD_ERROR;
293	<	painCave.isFatal = 1;
294	<	simError();
295	<	}
296	<	electrostaticAtomData.is_Charge = true;
297	<	electrostaticAtomData.charge = doubleData->getData();
298	<	}
309	>	// working variables for Taylor expansion:
310	>	RealType rmRc, rmRc2, rmRc3, rmRc4;
311
312	<	if (atomType->isDirectional()) {
313	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
314	<
315	<	if (daType->isDipole()) {
316	<	GenericData* data = daType->getPropertyByName("Dipole");
317	<
318	<	if (data == NULL) {
319	<	sprintf( painCave.errMsg,
320	<	"Electrostatic::addType could not find Dipole\n"
321	<	"\tparameters for atomType %s.\n",
322	<	daType->getName().c_str());
323	<	painCave.severity = OPENMD_ERROR;
324	<	painCave.isFatal = 1;
325	<	simError();
326	<	}
327	<
328	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
329	<	if (doubleData == NULL) {
330	<	sprintf( painCave.errMsg,
331	<	"Electrostatic::addType could not convert GenericData to "
332	<	"Dipole Moment\n"
333	<	"\tfor atom type %s\n", daType->getName().c_str());
334	<	painCave.severity = OPENMD_ERROR;
335	<	painCave.isFatal = 1;
336	<	simError();
337	<	}
338	<	electrostaticAtomData.is_Dipole = true;
339	<	electrostaticAtomData.dipole_moment = doubleData->getData();
312	>	// Approximate using splines using a maximum of 0.1 Angstroms
313	>	// between points.
314	>	int nptest = int((cutoffRadius_ + 2.0) / 0.1);
315	>	np_ = (np_ > nptest) ? np_ : nptest;
316	>
317	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
318	>	// have charged atoms longer than the cutoffRadius away from each
319	>	// other.  Splining is almost certainly the best choice here.
320	>	// Direct calls to erfc would be preferrable if it is a very fast
321	>	// implementation.
322	>
323	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_);
324	>
325	>	// Storage vectors for the computed functions
326	>	vector<RealType> rv;
327	>	vector<RealType> v01v;
328	>	vector<RealType> v11v;
329	>	vector<RealType> v21v, v22v;
330	>	vector<RealType> v31v, v32v;
331	>	vector<RealType> v41v, v42v, v43v;
332	>
333	>	for (int i = 1; i < np_ + 1; i++) {
334	>	r = RealType(i) * dx;
335	>	rv.push_back(r);
336	>
337	>	ri = 1.0 / r;
338	>	ri2 = ri * ri;
339	>
340	>	r2 = r * r;
341	>	expTerm = exp(-a2 * r2);
342	>
343	>	// Taylor expansion factors (no need for factorials this way):
344	>	rmRc = r - cutoffRadius_;
345	>	rmRc2 = rmRc  * rmRc / 2.0;
346	>	rmRc3 = rmRc2 * rmRc / 3.0;
347	>	rmRc4 = rmRc3 * rmRc / 4.0;
348	>
349	>	// values of Smith's B_l functions at r:
350	>	if (screeningMethod_ == DAMPED) {
351	>	b0 = erfc(dampingAlpha_ * r) * ri;
352	>	b1 = (      b0 +     2.0*a2     * expTerm * invArootPi) * ri2;
353	>	b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2;
354	>	b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2;
355	>	b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2;
356	>	b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2;
357	>	} else {
358	>	b0 = ri;
359	>	b1 = (      b0) * ri2;
360	>	b2 = (3.0 * b1) * ri2;
361	>	b3 = (5.0 * b2) * ri2;
362	>	b4 = (7.0 * b3) * ri2;
363	>	b5 = (9.0 * b4) * ri2;
364		}
365	+
366	+	// higher derivatives of B_0 at r:
367	+	db0_1 = -r * b1;
368	+	db0_2 =     -b1 + r2 * b2;
369	+	db0_3 =          3.0*r*b2   - r2*r*b3;
370	+	db0_4 =          3.0*b2   - 6.0*r2*b3     + r2*r2*b4;
371	+	db0_5 =                    -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5;
372
373	<	if (daType->isSplitDipole()) {
374	<	GenericData* data = daType->getPropertyByName("SplitDipoleDistance");
375	<
376	<	if (data == NULL) {
377	<	sprintf(painCave.errMsg,
378	<	"Electrostatic::addType could not find SplitDipoleDistance\n"
379	<	"\tparameter for atomType %s.\n",
380	<	daType->getName().c_str());
381	<	painCave.severity = OPENMD_ERROR;
382	<	painCave.isFatal = 1;
383	<	simError();
384	<	}
373	>	f = b0;
374	>	fc = b0c;
375	>	f0 = f - fc - rmRc*db0c_1;
376	>
377	>	g = db0_1;
378	>	gc = db0c_1;
379	>	g0 = g - gc;
380	>	g1 = g0 - rmRc *db0c_2;
381	>	g2 = g1 - rmRc2*db0c_3;
382	>	g3 = g2 - rmRc3*db0c_4;
383	>	g4 = g3 - rmRc4*db0c_5;
384	>
385	>	h = db0_2;
386	>	hc = db0c_2;
387	>	h1 = h - hc;
388	>	h2 = h1 - rmRc *db0c_3;
389	>	h3 = h2 - rmRc2*db0c_4;
390	>	h4 = h3 - rmRc3*db0c_5;
391	>
392	>	s = db0_3;
393	>	sc = db0c_3;
394	>	s2 = s - sc;
395	>	s3 = s2 - rmRc *db0c_4;
396	>	s4 = s3 - rmRc2*db0c_5;
397	>
398	>	t = db0_4;
399	>	tc = db0c_4;
400	>	t3 = t - tc;
401	>	t4 = t3 - rmRc *db0c_5;
402
403	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
404	<	if (doubleData == NULL) {
405	<	sprintf( painCave.errMsg,
346	<	"Electrostatic::addType could not convert GenericData to "
347	<	"SplitDipoleDistance for\n"
348	<	"\tatom type %s\n", daType->getName().c_str());
349	<	painCave.severity = OPENMD_ERROR;
350	<	painCave.isFatal = 1;
351	<	simError();
352	<	}
353	<	electrostaticAtomData.is_SplitDipole = true;
354	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
355	<	}
403	>	u = db0_5;
404	>	uc = db0c_5;
405	>	u4 = u - uc;
406
407	<	if (daType->isQuadrupole()) {
408	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
407	>	// in what follows below, the various v functions are used for
408	>	// potentials and torques, while the w functions show up in the
409	>	// forces.
410	>
411	>	switch (summationMethod_) {
412	>	case esm_SHIFTED_FORCE:
413	>
414	>	v01 = f - fc - rmRc*gc;
415	>	v11 = g - gc - rmRc*hc;
416	>	v21 = g*ri - gc*ric - rmRc*(hc - gc*ric)*ric;
417	>	v22 = h - g*ri - (hc - gc*ric) - rmRc*(sc - (hc - gc*ric)*ric);
418	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric - rmRc*(sc-2.0*(hc-gc*ric)*ric)*ric;
419	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric)
420	>	- rmRc*(tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
421	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2
422	>	- rmRc*(sc - 3.0*(hc-gc*ric)*ric)*ric2;
423	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric
424	>	- rmRc*(tc - (4.0*sc - 9.0*(hc - gc*ric)*ric)*ric)*ric;
425
426	<	if (data == NULL) {
427	<	sprintf( painCave.errMsg,
428	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
429	<	"\tparameter for atomType %s.\n",
430	<	daType->getName().c_str());
431	<	painCave.severity = OPENMD_ERROR;
432	<	painCave.isFatal = 1;
433	<	simError();
434	<	}
426	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
427	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric)
428	>	- rmRc*(uc-3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
429	>
430	>	dv01 = g - gc;
431	>	dv11 = h - hc;
432	>	dv21 = (h - g*ri)*ri - (hc - gc*ric)*ric;
433	>	dv22 = (s - (h - g*ri)*ri) - (sc - (hc - gc*ric)*ric);
434	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri - (sc - 2.0*(hc-gc*ric)*ric)*ric;
435	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri)
436	>	- (tc - 3.0*(sc-2.0*(hc-gc*ric)*ric)*ric);
437	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2 - (sc - 3.0*(hc - gc*ric)*ric)*ric2;
438	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri
439	>	- (tc - (4.0*sc - 9.0*(hc-gc*ric)*ric)*ric)*ric;
440	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri)
441	>	- (uc - 3.0*(2.0*tc - (7.0*sc - 15.0*(hc - gc*ric)*ric)*ric)*ric);
442
443	<	// Quadrupoles in OpenMD are set as the diagonal elements
371	<	// of the diagonalized traceless quadrupole moment tensor.
372	<	// The column vectors of the unitary matrix that diagonalizes
373	<	// the quadrupole moment tensor become the eFrame (or the
374	<	// electrostatic version of the body-fixed frame.
443	>	break;
444
445	<	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
446	<	if (v3dData == NULL) {
447	<	sprintf( painCave.errMsg,
448	<	"Electrostatic::addType could not convert GenericData to "
449	<	"Quadrupole Moments for\n"
450	<	"\tatom type %s\n", daType->getName().c_str());
451	<	painCave.severity = OPENMD_ERROR;
452	<	painCave.isFatal = 1;
453	<	simError();
445	>	case esm_TAYLOR_SHIFTED:
446	>
447	>	v01 = f0;
448	>	v11 = g1;
449	>	v21 = g2 * ri;
450	>	v22 = h2 - v21;
451	>	v31 = (h3 - g3 * ri) * ri;
452	>	v32 = s3 - 3.0*v31;
453	>	v41 = (h4 - g4 * ri) * ri2;
454	>	v42 = s4 * ri - 3.0*v41;
455	>	v43 = t4 - 6.0*v42 - 3.0*v41;
456	>
457	>	dv01 = g0;
458	>	dv11 = h1;
459	>	dv21 = (h2 - g2*ri)*ri;
460	>	dv22 = (s2 - (h2 - g2*ri)*ri);
461	>	dv31 = (s3 - 2.0*(h3-g3*ri)*ri)*ri;
462	>	dv32 = (t3 - 3.0*(s3-2.0*(h3-g3*ri)*ri)*ri);
463	>	dv41 = (s4 - 3.0*(h4 - g4*ri)*ri)*ri2;
464	>	dv42 = (t4 - (4.0*s4 - 9.0*(h4-g4*ri)*ri)*ri)*ri;
465	>	dv43 = (u4 - 3.0*(2.0*t4 - (7.0*s4 - 15.0*(h4 - g4*ri)*ri)*ri)*ri);
466	>
467	>	break;
468	>
469	>	case esm_SHIFTED_POTENTIAL:
470	>
471	>	v01 = f - fc;
472	>	v11 = g - gc;
473	>	v21 = g*ri - gc*ric;
474	>	v22 = h - g*ri - (hc - gc*ric);
475	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
476	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
477	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
478	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
479	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
480	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
481	>
482	>	dv01 = g;
483	>	dv11 = h;
484	>	dv21 = (h - g*ri)*ri;
485	>	dv22 = (s - (h - g*ri)*ri);
486	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
487	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
488	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
489	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
490	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
491	>
492	>	break;
493	>
494	>	case esm_SWITCHING_FUNCTION:
495	>	case esm_HARD:
496	>	case esm_EWALD_FULL:
497	>
498	>	v01 = f;
499	>	v11 = g;
500	>	v21 = g*ri;
501	>	v22 = h - g*ri;
502	>	v31 = (h-g*ri)*ri;
503	>	v32 = (s - 3.0*(h-g*ri)*ri);
504	>	v41 = (h - g*ri)*ri2;
505	>	v42 = (s-3.0*(h-g*ri)*ri)*ri;
506	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri);
507	>
508	>	dv01 = g;
509	>	dv11 = h;
510	>	dv21 = (h - g*ri)*ri;
511	>	dv22 = (s - (h - g*ri)*ri);
512	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
513	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
514	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
515	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
516	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
517	>
518	>	break;
519	>
520	>	case esm_REACTION_FIELD:
521	>
522	>	// following DL_POLY's lead for shifting the image charge potential:
523	>	f = b0 + preRF_ * r2;
524	>	fc = b0c + preRF_ * cutoffRadius_ * cutoffRadius_;
525	>
526	>	g = db0_1 + preRF_ * 2.0 * r;
527	>	gc = db0c_1 + preRF_ * 2.0 * cutoffRadius_;
528	>
529	>	h = db0_2 + preRF_ * 2.0;
530	>	hc = db0c_2 + preRF_ * 2.0;
531	>
532	>	v01 = f - fc;
533	>	v11 = g - gc;
534	>	v21 = g*ri - gc*ric;
535	>	v22 = h - g*ri - (hc - gc*ric);
536	>	v31 = (h-g*ri)*ri - (hc-gc*ric)*ric;
537	>	v32 = (s - 3.0*(h-g*ri)*ri) - (sc - 3.0*(hc-gc*ric)*ric);
538	>	v41 = (h - g*ri)*ri2 - (hc - gc*ric)*ric2;
539	>	v42 = (s-3.0*(h-g*ri)*ri)*ri - (sc-3.0*(hc-gc*ric)*ric)*ric;
540	>	v43 = (t - 3.0*(2.0*s - 5.0*(h - g*ri)*ri)*ri)
541	>	- (tc - 3.0*(2.0*sc - 5.0*(hc - gc*ric)*ric)*ric);
542	>
543	>	dv01 = g;
544	>	dv11 = h;
545	>	dv21 = (h - g*ri)*ri;
546	>	dv22 = (s - (h - g*ri)*ri);
547	>	dv31 = (s - 2.0*(h-g*ri)*ri)*ri;
548	>	dv32 = (t - 3.0*(s-2.0*(h-g*ri)*ri)*ri);
549	>	dv41 = (s - 3.0*(h - g*ri)*ri)*ri2;
550	>	dv42 = (t - (4.0*s - 9.0*(h-g*ri)*ri)*ri)*ri;
551	>	dv43 = (u - 3.0*(2.0*t - (7.0*s - 15.0*(h - g*ri)*ri)*ri)*ri);
552	>
553	>	break;
554	>
555	>	case esm_EWALD_PME:
556	>	case esm_EWALD_SPME:
557	>	default :
558	>	map<string, ElectrostaticSummationMethod>::iterator i;
559	>	std::string meth;
560	>	for (i = summationMap_.begin(); i != summationMap_.end(); ++i) {
561	>	if ((*i).second == summationMethod_) meth = (*i).first;
562		}
563	+	sprintf( painCave.errMsg,
564	+	"Electrostatic::initialize: electrostaticSummationMethod %s \n"
565	+	"\thas not been implemented yet. Please select one of:\n"
566	+	"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n",
567	+	meth.c_str() );
568	+	painCave.isFatal = 1;
569	+	simError();
570	+	break;
571	+	}
572	+
573	+	// Add these computed values to the storage vectors for spline creation:
574	+	v01v.push_back(v01);
575	+	v11v.push_back(v11);
576	+	v21v.push_back(v21);
577	+	v22v.push_back(v22);
578	+	v31v.push_back(v31);
579	+	v32v.push_back(v32);
580	+	v41v.push_back(v41);
581	+	v42v.push_back(v42);
582	+	v43v.push_back(v43);
583	+	}
584	+
585	+	// construct the spline structures and fill them with the values we've
586	+	// computed:
587	+
588	+	v01s = new CubicSpline();
589	+	v01s->addPoints(rv, v01v);
590	+	v11s = new CubicSpline();
591	+	v11s->addPoints(rv, v11v);
592	+	v21s = new CubicSpline();
593	+	v21s->addPoints(rv, v21v);
594	+	v22s = new CubicSpline();
595	+	v22s->addPoints(rv, v22v);
596	+	v31s = new CubicSpline();
597	+	v31s->addPoints(rv, v31v);
598	+	v32s = new CubicSpline();
599	+	v32s->addPoints(rv, v32v);
600	+	v41s = new CubicSpline();
601	+	v41s->addPoints(rv, v41v);
602	+	v42s = new CubicSpline();
603	+	v42s->addPoints(rv, v42v);
604	+	v43s = new CubicSpline();
605	+	v43s->addPoints(rv, v43v);
606	+
607	+	haveElectroSplines_ = true;
608	+
609	+	initialized_ = true;
610	+	}
611	+
612	+	void Electrostatic::addType(AtomType* atomType){
613	+
614	+	ElectrostaticAtomData electrostaticAtomData;
615	+	electrostaticAtomData.is_Charge = false;
616	+	electrostaticAtomData.is_Dipole = false;
617	+	electrostaticAtomData.is_Quadrupole = false;
618	+	electrostaticAtomData.is_Fluctuating = false;
619	+
620	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
621	+
622	+	if (fca.isFixedCharge()) {
623	+	electrostaticAtomData.is_Charge = true;
624	+	electrostaticAtomData.fixedCharge = fca.getCharge();
625	+	}
626	+
627	+	MultipoleAdapter ma = MultipoleAdapter(atomType);
628	+	if (ma.isMultipole()) {
629	+	if (ma.isDipole()) {
630	+	electrostaticAtomData.is_Dipole = true;
631	+	electrostaticAtomData.dipole = ma.getDipole();
632	+	}
633	+	if (ma.isQuadrupole()) {
634		electrostaticAtomData.is_Quadrupole = true;
635	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
635	>	electrostaticAtomData.quadrupole = ma.getQuadrupole();
636		}
637		}
638
639	<	AtomTypeProperties atp = atomType->getATP();
639	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
640
641	<	pair<map<int,AtomType*>::iterator,bool> ret;
642	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
641	>	if (fqa.isFluctuatingCharge()) {
642	>	electrostaticAtomData.is_Fluctuating = true;
643	>	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
644	>	electrostaticAtomData.hardness = fqa.getHardness();
645	>	electrostaticAtomData.slaterN = fqa.getSlaterN();
646	>	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
647	>	}
648	>
649	>	int atid = atomType->getIdent();
650	>	int etid = Etypes.size();
651	>	int fqtid = FQtypes.size();
652	>
653	>	pair<set<int>::iterator,bool> ret;
654	>	ret = Etypes.insert( atid );
655		if (ret.second == false) {
656		sprintf( painCave.errMsg,
657		"Electrostatic already had a previous entry with ident %d\n",
658	<	atp.ident);
658	>	atid);
659		painCave.severity = OPENMD_INFO;
660		painCave.isFatal = 0;
661		simError();
662		}
663
664	<	ElectrostaticMap[atomType] = electrostaticAtomData;
664	>	Etids[ atid ] = etid;
665	>	ElectrostaticMap.push_back(electrostaticAtomData);
666	>
667	>	if (electrostaticAtomData.is_Fluctuating) {
668	>	ret = FQtypes.insert( atid );
669	>	if (ret.second == false) {
670	>	sprintf( painCave.errMsg,
671	>	"Electrostatic already had a previous fluctuating charge entry with ident %d\n",
672	>	atid );
673	>	painCave.severity = OPENMD_INFO;
674	>	painCave.isFatal = 0;
675	>	simError();
676	>	}
677	>	FQtids[atid] = fqtid;
678	>	Jij[fqtid].resize(nFlucq_);
679	>
680	>	// Now, iterate over all known fluctuating and add to the coulomb integral map:
681	>
682	>	std::set<int>::iterator it;
683	>	for( it = FQtypes.begin(); it != FQtypes.end(); ++it) {
684	>	int etid2 = Etids[ (*it) ];
685	>	int fqtid2 = FQtids[ (*it) ];
686	>	ElectrostaticAtomData eaData2 = ElectrostaticMap[ etid2 ];
687	>	RealType a = electrostaticAtomData.slaterZeta;
688	>	RealType b = eaData2.slaterZeta;
689	>	int m = electrostaticAtomData.slaterN;
690	>	int n = eaData2.slaterN;
691	>
692	>	// Create the spline of the coulombic integral for s-type
693	>	// Slater orbitals.  Add a 2 angstrom safety window to deal
694	>	// with cutoffGroups that have charged atoms longer than the
695	>	// cutoffRadius away from each other.
696	>
697	>	RealType rval;
698	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
699	>	vector<RealType> rvals;
700	>	vector<RealType> Jvals;
701	>	// don't start at i = 0, as rval = 0 is undefined for the
702	>	// slater overlap integrals.
703	>	for (int i = 1; i < np_+1; i++) {
704	>	rval = RealType(i) * dr;
705	>	rvals.push_back(rval);
706	>	Jvals.push_back(sSTOCoulInt( a, b, m, n, rval *
707	>	PhysicalConstants::angstromToBohr ) *
708	>	PhysicalConstants::hartreeToKcal );
709	>	}
710	>
711	>	CubicSpline* J = new CubicSpline();
712	>	J->addPoints(rvals, Jvals);
713	>	Jij[fqtid][fqtid2] = J;
714	>	Jij[fqtid2].resize( nFlucq_ );
715	>	Jij[fqtid2][fqtid] = J;
716	>	}
717	>	}
718		return;
719		}
720
721	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
722	<	RealType theRSW ) {
410	<	cutoffRadius_ = theECR;
411	<	rrf_ = cutoffRadius_;
412	<	rt_ = theRSW;
721	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
722	>	cutoffRadius_ = rCut;
723		haveCutoffRadius_ = true;
724		}
725	+
726		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
727		summationMethod_ = esm;
728		}
#	Line 427 | Line 738 | namespace OpenMD {
738		haveDielectric_ = true;
739		}
740
741	<	void Electrostatic::calcForce(InteractionData idat) {
741	>	void Electrostatic::calcForce(InteractionData &idat) {
742
432	–	// utility variables.  Should clean these up and use the Vector3d and
433	–	// Mat3x3d to replace as many as we can in future versions:
434	–
435	–	RealType q_i, q_j, mu_i, mu_j, d_i, d_j;
436	–	RealType qxx_i, qyy_i, qzz_i;
437	–	RealType qxx_j, qyy_j, qzz_j;
438	–	RealType cx_i, cy_i, cz_i;
439	–	RealType cx_j, cy_j, cz_j;
440	–	RealType cx2, cy2, cz2;
441	–	RealType ct_i, ct_j, ct_ij, a1;
442	–	RealType riji, ri, ri2, ri3, ri4;
443	–	RealType pref, vterm, epot, dudr;
444	–	RealType scale, sc2;
445	–	RealType pot_term, preVal, rfVal;
446	–	RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
447	–	RealType preSw, preSwSc;
448	–	RealType c1, c2, c3, c4;
449	–	RealType erfcVal, derfcVal;
450	–	RealType BigR;
451	–
452	–	Vector3d Q_i, Q_j;
453	–	Vector3d ux_i, uy_i, uz_i;
454	–	Vector3d ux_j, uy_j, uz_j;
455	–	Vector3d dudux_i, duduy_i, duduz_i;
456	–	Vector3d dudux_j, duduy_j, duduz_j;
457	–	Vector3d rhatdot2, rhatc4;
458	–	Vector3d dVdr;
459	–
460	–	pair<RealType, RealType> res;
461	–
743		if (!initialized_) initialize();
744
745	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
746	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
466	<
467	<	// some variables we'll need independent of electrostatic type:
745	>	data1 = ElectrostaticMap[Etids[idat.atid1]];
746	>	data2 = ElectrostaticMap[Etids[idat.atid2]];
747
748	<	riji = 1.0 / idat.rij;
749	<	Vector3d rhat = idat.d  * riji;
750	<
751	<	// logicals
752	<
753	<	bool i_is_Charge = data1.is_Charge;
754	<	bool i_is_Dipole = data1.is_Dipole;
755	<	bool i_is_SplitDipole = data1.is_SplitDipole;
477	<	bool i_is_Quadrupole = data1.is_Quadrupole;
478	<
479	<	bool j_is_Charge = data2.is_Charge;
480	<	bool j_is_Dipole = data2.is_Dipole;
481	<	bool j_is_SplitDipole = data2.is_SplitDipole;
482	<	bool j_is_Quadrupole = data2.is_Quadrupole;
748	>	U = 0.0;  // Potential
749	>	F.zero();  // Force
750	>	Ta.zero(); // Torque on site a
751	>	Tb.zero(); // Torque on site b
752	>	Ea.zero(); // Electric field at site a
753	>	Eb.zero(); // Electric field at site b
754	>	dUdCa = 0.0; // fluctuating charge force at site a
755	>	dUdCb = 0.0; // fluctuating charge force at site a
756
757	<	if (i_is_Charge)
758	<	q_i = data1.charge;
757	>	// Indirect interactions mediated by the reaction field.
758	>	indirect_Pot = 0.0;   // Potential
759	>	indirect_F.zero();    // Force
760	>	indirect_Ta.zero();   // Torque on site a
761	>	indirect_Tb.zero();   // Torque on site b
762
763	<	if (i_is_Dipole) {
764	<	mu_i = data1.dipole_moment;
489	<	uz_i = idat.eFrame1.getColumn(2);
490	<
491	<	ct_i = dot(uz_i, rhat);
763	>	// Excluded potential that is still computed for fluctuating charges
764	>	excluded_Pot= 0.0;
765
766	<	if (i_is_SplitDipole)
767	<	d_i = data1.split_dipole_distance;
766	>
767	>	// some variables we'll need independent of electrostatic type:
768	>
769	>	ri = 1.0 /  *(idat.rij);
770	>	rhat =  *(idat.d)  * ri;
771
772	<	duduz_i = V3Zero;
497	<	}
498	<
499	<	if (i_is_Quadrupole) {
500	<	Q_i = data1.quadrupole_moments;
501	<	qxx_i = Q_i.x();
502	<	qyy_i = Q_i.y();
503	<	qzz_i = Q_i.z();
504	<
505	<	ux_i = idat.eFrame1.getColumn(0);
506	<	uy_i = idat.eFrame1.getColumn(1);
507	<	uz_i = idat.eFrame1.getColumn(2);
772	>	// logicals
773
774	<	cx_i = dot(ux_i, rhat);
775	<	cy_i = dot(uy_i, rhat);
776	<	cz_i = dot(uz_i, rhat);
774	>	a_is_Charge = data1.is_Charge;
775	>	a_is_Dipole = data1.is_Dipole;
776	>	a_is_Quadrupole = data1.is_Quadrupole;
777	>	a_is_Fluctuating = data1.is_Fluctuating;
778
779	<	dudux_i = V3Zero;
780	<	duduy_i = V3Zero;
781	<	duduz_i = V3Zero;
779	>	b_is_Charge = data2.is_Charge;
780	>	b_is_Dipole = data2.is_Dipole;
781	>	b_is_Quadrupole = data2.is_Quadrupole;
782	>	b_is_Fluctuating = data2.is_Fluctuating;
783	>
784	>	// Obtain all of the required radial function values from the
785	>	// spline structures:
786	>
787	>	// needed for fields (and forces):
788	>	if (a_is_Charge || b_is_Charge) {
789	>	v01s->getValueAndDerivativeAt( *(idat.rij), v01, dv01);
790		}
791	+	if (a_is_Dipole || b_is_Dipole) {
792	+	v11s->getValueAndDerivativeAt( *(idat.rij), v11, dv11);
793	+	v11or = ri * v11;
794	+	}
795	+	if (a_is_Quadrupole || b_is_Quadrupole ||  (a_is_Dipole && b_is_Dipole)) {
796	+	v21s->getValueAndDerivativeAt( *(idat.rij), v21, dv21);
797	+	v22s->getValueAndDerivativeAt( *(idat.rij), v22, dv22);
798	+	v22or = ri * v22;
799	+	}
800
801	<	if (j_is_Charge)
802	<	q_j = data2.charge;
801	>	// needed for potentials (and forces and torques):
802	>	if ((a_is_Dipole && b_is_Quadrupole) ||
803	>	(b_is_Dipole && a_is_Quadrupole)) {
804	>	v31s->getValueAndDerivativeAt( *(idat.rij), v31, dv31);
805	>	v32s->getValueAndDerivativeAt( *(idat.rij), v32, dv32);
806	>	v31or = v31 * ri;
807	>	v32or = v32 * ri;
808	>	}
809	>	if (a_is_Quadrupole && b_is_Quadrupole) {
810	>	v41s->getValueAndDerivativeAt( *(idat.rij), v41, dv41);
811	>	v42s->getValueAndDerivativeAt( *(idat.rij), v42, dv42);
812	>	v43s->getValueAndDerivativeAt( *(idat.rij), v43, dv43);
813	>	v42or = v42 * ri;
814	>	v43or = v43 * ri;
815	>	}
816
817	<	if (j_is_Dipole) {
818	<	mu_j = data2.dipole_moment;
819	<	uz_j = idat.eFrame2.getColumn(2);
817	>	// calculate the single-site contributions (fields, etc).
818	>
819	>	if (a_is_Charge) {
820	>	C_a = data1.fixedCharge;
821
822	<	ct_j = dot(uz_j, rhat);
823	<
824	<	if (j_is_SplitDipole)
528	<	d_j = data2.split_dipole_distance;
822	>	if (a_is_Fluctuating) {
823	>	C_a += *(idat.flucQ1);
824	>	}
825
826	<	duduz_j = V3Zero;
826	>	if (idat.excluded) {
827	>	*(idat.skippedCharge2) += C_a;
828	>	} else {
829	>	// only do the field if we're not excluded:
830	>	Eb -= C_a *  pre11_ * dv01 * rhat;
831	>	}
832		}
833
834	<	if (j_is_Quadrupole) {
835	<	Q_j = data2.quadrupole_moments;
836	<	qxx_j = Q_j.x();
837	<	qyy_j = Q_j.y();
838	<	qzz_j = Q_j.z();
834	>	if (a_is_Dipole) {
835	>	D_a = *(idat.dipole1);
836	>	rdDa = dot(rhat, D_a);
837	>	rxDa = cross(rhat, D_a);
838	>	if (!idat.excluded)
839	>	Eb -=  pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
840	>	}
841	>
842	>	if (a_is_Quadrupole) {
843	>	Q_a = *(idat.quadrupole1);
844	>	trQa =  Q_a.trace();
845	>	Qar =   Q_a * rhat;
846	>	rQa = rhat * Q_a;
847	>	rdQar = dot(rhat, Qar);
848	>	rxQar = cross(rhat, Qar);
849	>	if (!idat.excluded)
850	>	Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or
851	>	+ rdQar * rhat * (dv22 - 2.0*v22or));
852	>	}
853	>
854	>	if (b_is_Charge) {
855	>	C_b = data2.fixedCharge;
856
857	<	ux_j = idat.eFrame2.getColumn(0);
858	<	uy_j = idat.eFrame2.getColumn(1);
859	<	uz_j = idat.eFrame2.getColumn(2);
860	<
861	<	cx_j = dot(ux_j, rhat);
862	<	cy_j = dot(uy_j, rhat);
863	<	cz_j = dot(uz_j, rhat);
864	<
865	<	dudux_j = V3Zero;
548	<	duduy_j = V3Zero;
549	<	duduz_j = V3Zero;
857	>	if (b_is_Fluctuating)
858	>	C_b += *(idat.flucQ2);
859	>
860	>	if (idat.excluded) {
861	>	*(idat.skippedCharge1) += C_b;
862	>	} else {
863	>	// only do the field if we're not excluded:
864	>	Ea += C_b *  pre11_ * dv01 * rhat;
865	>	}
866		}
867
868	<	epot = 0.0;
869	<	dVdr = V3Zero;
868	>	if (b_is_Dipole) {
869	>	D_b = *(idat.dipole2);
870	>	rdDb = dot(rhat, D_b);
871	>	rxDb = cross(rhat, D_b);
872	>	if (!idat.excluded)
873	>	Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b);
874	>	}
875
876	<	if (i_is_Charge) {
876	>	if (b_is_Quadrupole) {
877	>	Q_b = *(idat.quadrupole2);
878	>	trQb =  Q_b.trace();
879	>	Qbr =   Q_b * rhat;
880	>	rQb = rhat * Q_b;
881	>	rdQbr = dot(rhat, Qbr);
882	>	rxQbr = cross(rhat, Qbr);
883	>	if (!idat.excluded)
884	>	Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or
885	>	+ rdQbr * rhat * (dv22 - 2.0*v22or));
886	>	}
887	>
888	>	if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) {
889	>	J = Jij[FQtids[idat.atid1]][FQtids[idat.atid2]];
890	>	}
891	>
892	>	if (a_is_Charge) {
893
894	<	if (j_is_Charge) {
895	<	if (screeningMethod_ == DAMPED) {
896	<	// assemble the damping variables
897	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
898	<	erfcVal = res.first;
899	<	derfcVal = res.second;
900	<	c1 = erfcVal * riji;
564	<	c2 = (-derfcVal + c1) * riji;
565	<	} else {
566	<	c1 = riji;
567	<	c2 = c1 * riji;
568	<	}
894	>	if (b_is_Charge) {
895	>	pref =  pre11_ * *(idat.electroMult);
896	>	U  += C_a * C_b * pref * v01;
897	>	F  += C_a * C_b * pref * dv01 * rhat;
898	>
899	>	// If this is an excluded pair, there are still indirect
900	>	// interactions via the reaction field we must worry about:
901
902	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
902	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
903	>	rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2);
904	>	indirect_Pot += rfContrib;
905	>	indirect_F   += rfContrib * 2.0 * ri * rhat;
906	>	}
907
908	<	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
909	<	vterm = preVal * (c1 - c1c_);
910	<	dudr  = -idat.sw * preVal * c2;
908	>	// Fluctuating charge forces are handled via Coulomb integrals
909	>	// for excluded pairs (i.e. those connected via bonds) and
910	>	// with the standard charge-charge interaction otherwise.
911
912	<	} else if (summationMethod_ == esm_SHIFTED_FORCE)  {
913	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - cutoffRadius_) );
914	<	dudr  = idat.sw * preVal * (c2c_ - c2);
915	<
916	<	} else if (summationMethod_ == esm_REACTION_FIELD) {
917	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
918	<	vterm = preVal * ( riji + rfVal );
583	<	dudr  = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
584	<
912	>	if (idat.excluded) {
913	>	if (a_is_Fluctuating || b_is_Fluctuating) {
914	>	coulInt = J->getValueAt( *(idat.rij) );
915	>	if (a_is_Fluctuating)  dUdCa += coulInt * C_b;
916	>	if (b_is_Fluctuating)  dUdCb += coulInt * C_a;
917	>	excluded_Pot += C_a * C_b * coulInt;
918	>	}
919		} else {
920	<	vterm = preVal * riji * erfcVal;
921	<
588	<	dudr  = - idat.sw * preVal * c2;
589	<
920	>	if (a_is_Fluctuating) dUdCa += C_b * pref * v01;
921	>	if (a_is_Fluctuating) dUdCb += C_a * pref * v01;
922		}
591	–
592	–	idat.vpair += vterm;
593	–	epot += idat.sw * vterm;
594	–
595	–	dVdr += dudr * rhat;
923		}
924
925	<	if (j_is_Dipole) {
926	<	// pref is used by all the possible methods
927	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
928	<	preSw = idat.sw * pref;
925	>	if (b_is_Dipole) {
926	>	pref =  pre12_ * *(idat.electroMult);
927	>	U  += C_a * pref * v11 * rdDb;
928	>	F  += C_a * pref * ((dv11 - v11or) * rdDb * rhat + v11or * D_b);
929	>	Tb += C_a * pref * v11 * rxDb;
930
931	<	if (summationMethod_ == esm_REACTION_FIELD) {
604	<	ri2 = riji * riji;
605	<	ri3 = ri2 * riji;
606	<
607	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
608	<	idat.vpair += vterm;
609	<	epot += idat.sw * vterm;
931	>	if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb;
932
933	<	dVdr +=  -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
934	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
933	>	// Even if we excluded this pair from direct interactions, we
934	>	// still have the reaction-field-mediated charge-dipole
935	>	// interaction:
936
937	<	} else {
938	<	// determine the inverse r used if we have split dipoles
939	<	if (j_is_SplitDipole) {
940	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
941	<	ri = 1.0 / BigR;
619	<	scale = idat.rij * ri;
620	<	} else {
621	<	ri = riji;
622	<	scale = 1.0;
623	<	}
624	<
625	<	sc2 = scale * scale;
626	<
627	<	if (screeningMethod_ == DAMPED) {
628	<	// assemble the damping variables
629	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
630	<	erfcVal = res.first;
631	<	derfcVal = res.second;
632	<	c1 = erfcVal * ri;
633	<	c2 = (-derfcVal + c1) * ri;
634	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
635	<	} else {
636	<	c1 = ri;
637	<	c2 = c1 * ri;
638	<	c3 = 3.0 * c2 * ri;
639	<	}
640	<
641	<	c2ri = c2 * ri;
642	<
643	<	// calculate the potential
644	<	pot_term =  scale * c2;
645	<	vterm = -pref * ct_j * pot_term;
646	<	idat.vpair += vterm;
647	<	epot += idat.sw * vterm;
648	<
649	<	// calculate derivatives for forces and torques
650	<
651	<	dVdr += -preSw * (uz_j * c2ri - ct_j * rhat * sc2 * c3);
652	<	duduz_j += -preSw * pot_term * rhat;
653	<
937	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
938	>	rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij);
939	>	indirect_Pot += rfContrib * rdDb;
940	>	indirect_F   += rfContrib * D_b / (*idat.rij);
941	>	indirect_Tb  += C_a * pref * preRF_ * rxDb;
942		}
943		}
944
945	<	if (j_is_Quadrupole) {
946	<	// first precalculate some necessary variables
947	<	cx2 = cx_j * cx_j;
948	<	cy2 = cy_j * cy_j;
949	<	cz2 = cz_j * cz_j;
950	<	pref =  idat.electroMult * pre14_ * q_i * one_third_;
663	<
664	<	if (screeningMethod_ == DAMPED) {
665	<	// assemble the damping variables
666	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
667	<	erfcVal = res.first;
668	<	derfcVal = res.second;
669	<	c1 = erfcVal * riji;
670	<	c2 = (-derfcVal + c1) * riji;
671	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
672	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
673	<	} else {
674	<	c1 = riji;
675	<	c2 = c1 * riji;
676	<	c3 = 3.0 * c2 * riji;
677	<	c4 = 5.0 * c3 * riji * riji;
678	<	}
945	>	if (b_is_Quadrupole) {
946	>	pref = pre14_ * *(idat.electroMult);
947	>	U  +=  C_a * pref * (v21 * trQb + v22 * rdQbr);
948	>	F  +=  C_a * pref * (trQb * dv21 * rhat + 2.0 * Qbr * v22or);
949	>	F  +=  C_a * pref * rdQbr * rhat * (dv22 - 2.0*v22or);
950	>	Tb +=  C_a * pref * 2.0 * rxQbr * v22;
951
952	<	// precompute variables for convenience
681	<	preSw = idat.sw * pref;
682	<	c2ri = c2 * riji;
683	<	c3ri = c3 * riji;
684	<	c4rij = c4 * idat.rij;
685	<	rhatdot2 = 2.0 * rhat * c3;
686	<	rhatc4 = rhat * c4rij;
687	<
688	<	// calculate the potential
689	<	pot_term = ( qxx_j * (cx2*c3 - c2ri) +
690	<	qyy_j * (cy2*c3 - c2ri) +
691	<	qzz_j * (cz2*c3 - c2ri) );
692	<	vterm = pref * pot_term;
693	<	idat.vpair += vterm;
694	<	epot += idat.sw * vterm;
695	<
696	<	// calculate derivatives for the forces and torques
697	<
698	<	dVdr += -preSw * ( qxx_j* (cx2*rhatc4 - (2.0*cx_j*ux_j + rhat)*c3ri) +
699	<	qyy_j* (cy2*rhatc4 - (2.0*cy_j*uy_j + rhat)*c3ri) +
700	<	qzz_j* (cz2*rhatc4 - (2.0*cz_j*uz_j + rhat)*c3ri));
701	<
702	<	dudux_j += preSw * qxx_j * cx_j * rhatdot2;
703	<	duduy_j += preSw * qyy_j * cy_j * rhatdot2;
704	<	duduz_j += preSw * qzz_j * cz_j * rhatdot2;
952	>	if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr);
953		}
954		}
707	–
708	–	if (i_is_Dipole) {
955
956	<	if (j_is_Charge) {
711	<	// variables used by all the methods
712	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
713	<	preSw = idat.sw * pref;
956	>	if (a_is_Dipole) {
957
958	<	if (summationMethod_ == esm_REACTION_FIELD) {
958	>	if (b_is_Charge) {
959	>	pref = pre12_ * *(idat.electroMult);
960
961	<	ri2 = riji * riji;
962	<	ri3 = ri2 * riji;
961	>	U  -= C_b * pref * v11 * rdDa;
962	>	F  -= C_b * pref * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
963	>	Ta -= C_b * pref * v11 * rxDa;
964
965	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
721	<	idat.vpair += vterm;
722	<	epot += idat.sw * vterm;
723	<
724	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
725	<
726	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
727	<
728	<	} else {
729	<
730	<	// determine inverse r if we are using split dipoles
731	<	if (i_is_SplitDipole) {
732	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
733	<	ri = 1.0 / BigR;
734	<	scale = idat.rij * ri;
735	<	} else {
736	<	ri = riji;
737	<	scale = 1.0;
738	<	}
739	<
740	<	sc2 = scale * scale;
741	<
742	<	if (screeningMethod_ == DAMPED) {
743	<	// assemble the damping variables
744	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
745	<	erfcVal = res.first;
746	<	derfcVal = res.second;
747	<	c1 = erfcVal * ri;
748	<	c2 = (-derfcVal + c1) * ri;
749	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
750	<	} else {
751	<	c1 = ri;
752	<	c2 = c1 * ri;
753	<	c3 = 3.0 * c2 * ri;
754	<	}
755	<
756	<	c2ri = c2 * ri;
757	<
758	<	// calculate the potential
759	<	pot_term = c2 * scale;
760	<	vterm = pref * ct_i * pot_term;
761	<	idat.vpair += vterm;
762	<	epot += idat.sw * vterm;
965	>	if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa;
966
967	<	// calculate derivatives for the forces and torques
968	<	dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
969	<	duduz_i += preSw * pot_term * rhat;
967	>	// Even if we excluded this pair from direct interactions,
968	>	// we still have the reaction-field-mediated charge-dipole
969	>	// interaction:
970	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
971	>	rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij);
972	>	indirect_Pot -= rfContrib * rdDa;
973	>	indirect_F   -= rfContrib * D_a / (*idat.rij);
974	>	indirect_Ta  -= C_b * pref * preRF_ * rxDa;
975		}
976		}
977
978	<	if (j_is_Dipole) {
979	<	// variables used by all methods
980	<	ct_ij = dot(uz_i, uz_j);
978	>	if (b_is_Dipole) {
979	>	pref = pre22_ * *(idat.electroMult);
980	>	DadDb = dot(D_a, D_b);
981	>	DaxDb = cross(D_a, D_b);
982
983	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
984	<	preSw = idat.sw * pref;
983	>	U  -= pref * (DadDb * v21 + rdDa * rdDb * v22);
984	>	F  -= pref * (dv21 * DadDb * rhat + v22or * (rdDb * D_a + rdDa * D_b));
985	>	F  -= pref * (rdDa * rdDb) * (dv22 - 2.0*v22or) * rhat;
986	>	Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa);
987	>	Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb);
988
989	<	if (summationMethod_ == esm_REACTION_FIELD) {
990	<	ri2 = riji * riji;
991	<	ri3 = ri2 * riji;
992	<	ri4 = ri2 * ri2;
989	>	// Even if we excluded this pair from direct interactions, we
990	>	// still have the reaction-field-mediated dipole-dipole
991	>	// interaction:
992	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
993	>	rfContrib = -pref * preRF_ * 2.0;
994	>	indirect_Pot += rfContrib * DadDb;
995	>	indirect_Ta  += rfContrib * DaxDb;
996	>	indirect_Tb  -= rfContrib * DaxDb;
997	>	}
998	>	}
999
1000	<	vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
1001	<	preRF2_ * ct_ij );
1002	<	idat.vpair += vterm;
1003	<	epot += idat.sw * vterm;
1004	<
787	<	a1 = 5.0 * ct_i * ct_j - ct_ij;
788	<
789	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
1000	>	if (b_is_Quadrupole) {
1001	>	pref = pre24_ * *(idat.electroMult);
1002	>	DadQb = D_a * Q_b;
1003	>	DadQbr = dot(D_a, Qbr);
1004	>	DaxQbr = cross(D_a, Qbr);
1005
1006	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
1007	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
1008	<
1009	<	} else {
1010	<
1011	<	if (i_is_SplitDipole) {
1012	<	if (j_is_SplitDipole) {
1013	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
1014	<	} else {
1015	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
801	<	}
802	<	ri = 1.0 / BigR;
803	<	scale = idat.rij * ri;
804	<	} else {
805	<	if (j_is_SplitDipole) {
806	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
807	<	ri = 1.0 / BigR;
808	<	scale = idat.rij * ri;
809	<	} else {
810	<	ri = riji;
811	<	scale = 1.0;
812	<	}
813	<	}
814	<	if (screeningMethod_ == DAMPED) {
815	<	// assemble damping variables
816	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
817	<	erfcVal = res.first;
818	<	derfcVal = res.second;
819	<	c1 = erfcVal * ri;
820	<	c2 = (-derfcVal + c1) * ri;
821	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
822	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * ri * ri;
823	<	} else {
824	<	c1 = ri;
825	<	c2 = c1 * ri;
826	<	c3 = 3.0 * c2 * ri;
827	<	c4 = 5.0 * c3 * ri * ri;
828	<	}
1006	>	U  -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32);
1007	>	F  -= pref * (trQb*D_a + 2.0*DadQb) * v31or;
1008	>	F  -= pref * (trQb*rdDa + 2.0*DadQbr) * (dv31-v31or) * rhat;
1009	>	F  -= pref * (D_a*rdQbr + 2.0*rdDa*rQb) * v32or;
1010	>	F  -= pref * (rdDa * rdQbr * rhat * (dv32-3.0*v32or));
1011	>	Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32);
1012	>	Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31
1013	>	- 2.0*rdDa*rxQbr*v32);
1014	>	}
1015	>	}
1016
1017	<	// precompute variables for convenience
1018	<	sc2 = scale * scale;
1019	<	cti3 = ct_i * sc2 * c3;
1020	<	ctj3 = ct_j * sc2 * c3;
1021	<	ctidotj = ct_i * ct_j * sc2;
1022	<	preSwSc = preSw * scale;
1023	<	c2ri = c2 * ri;
837	<	c3ri = c3 * ri;
838	<	c4rij = c4 * idat.rij;
1017	>	if (a_is_Quadrupole) {
1018	>	if (b_is_Charge) {
1019	>	pref = pre14_ * *(idat.electroMult);
1020	>	U  += C_b * pref * (v21 * trQa + v22 * rdQar);
1021	>	F  += C_b * pref * (trQa * rhat * dv21 + 2.0 * Qar * v22or);
1022	>	F  += C_b * pref * rdQar * rhat * (dv22 - 2.0*v22or);
1023	>	Ta += C_b * pref * 2.0 * rxQar * v22;
1024
1025	<	// calculate the potential
1026	<	pot_term = (ct_ij * c2ri - ctidotj * c3);
1027	<	vterm = pref * pot_term;
1028	<	idat.vpair += vterm;
1029	<	epot += idat.sw * vterm;
1025	>	if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar);
1026	>	}
1027	>	if (b_is_Dipole) {
1028	>	pref = pre24_ * *(idat.electroMult);
1029	>	DbdQa = D_b * Q_a;
1030	>	DbdQar = dot(D_b, Qar);
1031	>	DbxQar = cross(D_b, Qar);
1032
1033	<	// calculate derivatives for the forces and torques
1034	<	dVdr += preSwSc * ( ctidotj * rhat * c4rij  -
1035	<	(ct_i*uz_j + ct_j*uz_i + ct_ij*rhat) * c3ri);
1036	<
1037	<	duduz_i += preSw * (uz_j * c2ri - ctj3 * rhat);
1038	<	duduz_j += preSw * (uz_i * c2ri - cti3 * rhat);
1039	<	}
1033	>	U  += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32);
1034	>	F  += pref * (trQa*D_b + 2.0*DbdQa) * v31or;
1035	>	F  += pref * (trQa*rdDb + 2.0*DbdQar) * (dv31-v31or) * rhat;
1036	>	F  += pref * (D_b*rdQar + 2.0*rdDb*rQa) * v32or;
1037	>	F  += pref * (rdDb * rdQar * rhat * (dv32-3.0*v32or));
1038	>	Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31
1039	>	+ 2.0*rdDb*rxQar*v32);
1040	>	Tb += pref * ((trQa*rxDb - 2.0 * DbxQar)*v31 + rxDb*rdQar*v32);
1041		}
1042	<	}
1042	>	if (b_is_Quadrupole) {
1043	>	pref = pre44_ * *(idat.electroMult);  // yes
1044	>	QaQb = Q_a * Q_b;
1045	>	trQaQb = QaQb.trace();
1046	>	rQaQb = rhat * QaQb;
1047	>	QaQbr = QaQb * rhat;
1048	>	QaxQb = cross(Q_a, Q_b);
1049	>	rQaQbr = dot(rQa, Qbr);
1050	>	rQaxQbr = cross(rQa, Qbr);
1051	>
1052	>	U  += pref * (trQa * trQb + 2.0 * trQaQb) * v41;
1053	>	U  += pref * (trQa * rdQbr + trQb * rdQar  + 4.0 * rQaQbr) * v42;
1054	>	U  += pref * (rdQar * rdQbr) * v43;
1055
1056	<	if (i_is_Quadrupole) {
1057	<	if (j_is_Charge) {
1058	<	// precompute some necessary variables
859	<	cx2 = cx_i * cx_i;
860	<	cy2 = cy_i * cy_i;
861	<	cz2 = cz_i * cz_i;
1056	>	F  += pref * rhat * (trQa * trQb + 2.0 * trQaQb)*dv41;
1057	>	F  += pref*rhat*(trQa*rdQbr + trQb*rdQar + 4.0*rQaQbr)*(dv42-2.0*v42or);
1058	>	F  += pref * rhat * (rdQar * rdQbr)*(dv43 - 4.0*v43or);
1059
1060	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
1060	>	F  += pref * 2.0 * (trQb*rQa + trQa*rQb) * v42or;
1061	>	F  += pref * 4.0 * (rQaQb + QaQbr) * v42or;
1062	>	F  += pref * 2.0 * (rQa*rdQbr + rdQar*rQb) * v43or;
1063
1064	<	if (screeningMethod_ == DAMPED) {
1065	<	// assemble the damping variables
1066	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
1067	<	erfcVal = res.first;
1068	<	derfcVal = res.second;
870	<	c1 = erfcVal * riji;
871	<	c2 = (-derfcVal + c1) * riji;
872	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
873	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
874	<	} else {
875	<	c1 = riji;
876	<	c2 = c1 * riji;
877	<	c3 = 3.0 * c2 * riji;
878	<	c4 = 5.0 * c3 * riji * riji;
879	<	}
880	<
881	<	// precompute some variables for convenience
882	<	preSw = idat.sw * pref;
883	<	c2ri = c2 * riji;
884	<	c3ri = c3 * riji;
885	<	c4rij = c4 * idat.rij;
886	<	rhatdot2 = 2.0 * rhat * c3;
887	<	rhatc4 = rhat * c4rij;
1064	>	Ta += pref * (- 4.0 * QaxQb * v41);
1065	>	Ta += pref * (- 2.0 * trQb * cross(rQa, rhat)
1066	>	+ 4.0 * cross(rhat, QaQbr)
1067	>	- 4.0 * rQaxQbr) * v42;
1068	>	Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43;
1069
889	–	// calculate the potential
890	–	pot_term = ( qxx_i * (cx2 * c3 - c2ri) +
891	–	qyy_i * (cy2 * c3 - c2ri) +
892	–	qzz_i * (cz2 * c3 - c2ri) );
893	–
894	–	vterm = pref * pot_term;
895	–	idat.vpair += vterm;
896	–	epot += idat.sw * vterm;
1070
1071	<	// calculate the derivatives for the forces and torques
1071	>	Tb += pref * (+ 4.0 * QaxQb * v41);
1072	>	Tb += pref * (- 2.0 * trQa * cross(rQb, rhat)
1073	>	- 4.0 * cross(rQaQb, rhat)
1074	>	+ 4.0 * rQaxQbr) * v42;
1075	>	// Possible replacement for line 2 above:
1076	>	//             + 4.0 * cross(rhat, QbQar)
1077
1078	<	dVdr += -preSw * (qxx_i* (cx2*rhatc4 - (2.0*cx_i*ux_i + rhat)*c3ri) +
901	<	qyy_i* (cy2*rhatc4 - (2.0*cy_i*uy_i + rhat)*c3ri) +
902	<	qzz_i* (cz2*rhatc4 - (2.0*cz_i*uz_i + rhat)*c3ri));
1078	>	Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43;
1079
904	–	dudux_i += preSw * qxx_i * cx_i *  rhatdot2;
905	–	duduy_i += preSw * qyy_i * cy_i *  rhatdot2;
906	–	duduz_i += preSw * qzz_i * cz_i *  rhatdot2;
1080		}
1081		}
1082
1083	<	idat.pot += epot;
1084	<	idat.f1 += dVdr;
1085	<
913	<	if (i_is_Dipole || i_is_Quadrupole)
914	<	idat.t1 -= cross(uz_i, duduz_i);
915	<	if (i_is_Quadrupole) {
916	<	idat.t1 -= cross(ux_i, dudux_i);
917	<	idat.t1 -= cross(uy_i, duduy_i);
1083	>	if (idat.doElectricField) {
1084	>	*(idat.eField1) += Ea * *(idat.electroMult);
1085	>	*(idat.eField2) += Eb * *(idat.electroMult);
1086		}
1087
1088	<	if (j_is_Dipole || j_is_Quadrupole)
1089	<	idat.t2 -= cross(uz_j, duduz_j);
922	<	if (j_is_Quadrupole) {
923	<	idat.t2 -= cross(uz_j, dudux_j);
924	<	idat.t2 -= cross(uz_j, duduy_j);
925	<	}
1088	>	if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1089	>	if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1090
1091	<	return;
1092	<	}
1091	>	if (!idat.excluded) {
1092	>
1093	>	*(idat.vpair) += U;
1094	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw);
1095	>	*(idat.f1) += F * *(idat.sw);
1096	>
1097	>	if (a_is_Dipole || a_is_Quadrupole)
1098	>	*(idat.t1) += Ta * *(idat.sw);
1099
1100	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
1100	>	if (b_is_Dipole || b_is_Quadrupole)
1101	>	*(idat.t2) += Tb * *(idat.sw);
1102	>
1103	>	} else {
1104
1105	<	if (!initialized_) initialize();
1105	>	// only accumulate the forces and torques resulting from the
1106	>	// indirect reaction field terms.
1107	>
1108	>	*(idat.vpair) += indirect_Pot;
1109	>	(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] +=  excluded_Pot;
1110	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot;
1111	>	*(idat.f1) += *(idat.sw) * indirect_F;
1112	>
1113	>	if (a_is_Dipole || a_is_Quadrupole)
1114	>	*(idat.t1) += *(idat.sw) * indirect_Ta;
1115	>
1116	>	if (b_is_Dipole || b_is_Quadrupole)
1117	>	*(idat.t2) += *(idat.sw) * indirect_Tb;
1118	>	}
1119	>	return;
1120	>	}
1121
1122	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
935	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
936	<
937	<	// logicals
1122	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1123
1124	<	bool i_is_Charge = data1.is_Charge;
940	<	bool i_is_Dipole = data1.is_Dipole;
1124	>	if (!initialized_) initialize();
1125
1126	<	bool j_is_Charge = data2.is_Charge;
1127	<	bool j_is_Dipole = data2.is_Dipole;
1128	<
1129	<	RealType q_i, q_j;
1130	<
1131	<	// The skippedCharge computation is needed by the real-space cutoff methods
1132	<	// (i.e. shifted force and shifted potential)
1126	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[sdat.atid]];
1127	>
1128	>	// logicals
1129	>	bool i_is_Charge = data.is_Charge;
1130	>	bool i_is_Dipole = data.is_Dipole;
1131	>	bool i_is_Quadrupole = data.is_Quadrupole;
1132	>	bool i_is_Fluctuating = data.is_Fluctuating;
1133	>	RealType C_a = data.fixedCharge;
1134	>	RealType self(0.0), preVal, DdD, trQ, trQQ;
1135
1136	<	if (i_is_Charge) {
1137	<	q_i = data1.charge;
952	<	skdat.skippedCharge2 += q_i;
1136	>	if (i_is_Dipole) {
1137	>	DdD = data.dipole.lengthSquare();
1138		}
1139	<
1140	<	if (j_is_Charge) {
1141	<	q_j = data2.charge;
1142	<	skdat.skippedCharge1 += q_j;
1139	>
1140	>	if (i_is_Fluctuating) {
1141	>	C_a += *(sdat.flucQ);
1142	>	// dVdFQ is really a force, so this is negative the derivative
1143	>	*(sdat.dVdFQ) -=  *(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	<
962	<	if (summationMethod_ == esm_REACTION_FIELD) {
963	<	RealType riji, ri2, ri3;
964	<	RealType q_i, mu_i, ct_i;
965	<	RealType q_j, mu_j, ct_j;
966	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
967	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
968	<
969	<	// some variables we'll need independent of electrostatic type:
1148	>	switch (summationMethod_) {
1149	>	case esm_REACTION_FIELD:
1150
971	–	riji = 1.0 / skdat.rij;
972	–	rhat = skdat.d  * riji;
973	–
974	–	if (i_is_Dipole) {
975	–	mu_i = data1.dipole_moment;
976	–	uz_i = skdat.eFrame1.getColumn(2);
977	–	ct_i = dot(uz_i, rhat);
978	–	duduz_i = V3Zero;
979	–	}
980	–
981	–	if (j_is_Dipole) {
982	–	mu_j = data2.dipole_moment;
983	–	uz_j = skdat.eFrame2.getColumn(2);
984	–	ct_j = dot(uz_j, rhat);
985	–	duduz_j = V3Zero;
986	–	}
987	–
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;
994	<	dudr  = skdat.sw * preVal * 2.0 * rfVal * riji;
995	<	dVdr += dudr * rhat;
996	<	}
997	<
998	<	if (j_is_Dipole) {
999	<	ri2 = riji * riji;
1000	<	ri3 = ri2 * riji;
1001	<	pref = skdat.electroMult * pre12_ * q_i * mu_j;
1002	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
1003	<	myPot += skdat.sw * vterm;
1004	<	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
1005	<	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1006	<	}
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) {
1010	<	ri2 = riji * riji;
1011	<	ri3 = ri2 * riji;
1012	<	pref = skdat.electroMult * pre12_ * q_j * mu_i;
1013	<	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
1014	<	myPot += skdat.sw * vterm;
1015	<	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
1016	<	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1017	<	}
1160	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DdD;
1161		}
1162
1163	<	// accumulate the forces and torques resulting from the self term
1021	<	skdat.pot += myPot;
1022	<	skdat.f1 += dVdr;
1163	>	break;
1164
1165	+	case esm_SHIFTED_FORCE:
1166	+	case esm_SHIFTED_POTENTIAL:
1167	+	case esm_TAYLOR_SHIFTED:
1168	+	if (i_is_Charge)
1169	+	self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge));
1170		if (i_is_Dipole)
1171	<	skdat.t1 -= cross(uz_i, duduz_i);
1172	<	if (j_is_Dipole)
1173	<	skdat.t2 -= cross(uz_j, duduz_j);
1171	>	self += selfMult2_ * pre22_ * DdD;
1172	>	if (i_is_Quadrupole) {
1173	>	trQ = data.quadrupole.trace();
1174	>	trQQ = (data.quadrupole * data.quadrupole).trace();
1175	>	self += selfMult4_ * pre44_ * (2.0*trQQ + trQ*trQ);
1176	>	if (i_is_Charge)
1177	>	self -= selfMult2_ * pre14_ * 2.0 * C_a * trQ;
1178	>	}
1179	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1180	>	break;
1181	>	default:
1182	>	break;
1183		}
1184		}
1185	+
1186	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
1187	+	// This seems to work moderately well as a default.  There's no
1188	+	// inherent scale for 1/r interactions that we can standardize.
1189	+	// 12 angstroms seems to be a reasonably good guess for most
1190	+	// cases.
1191	+	return 12.0;
1192	+	}
1193	+
1194	+
1195	+	void Electrostatic::ReciprocalSpaceSum () {
1196
1197	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1198	<	RealType mu1, preVal, chg1, self;
1197	>	RealType kPot = 0.0;
1198	>	RealType kVir = 0.0;
1199
1200	<	if (!initialized_) initialize();
1200	>	const RealType mPoleConverter = 0.20819434; // converts from the
1201	>	// internal units of
1202	>	// Debye (for dipoles)
1203	>	// or Debye-angstroms
1204	>	// (for quadrupoles) to
1205	>	// electron angstroms or
1206	>	// electron-angstroms^2
1207
1208	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1209	<
1210	<	// logicals
1208	>	const RealType eConverter = 332.0637778; // convert the
1209	>	// Charge-Charge
1210	>	// electrostatic
1211	>	// interactions into kcal /
1212	>	// mol assuming distances
1213	>	// are measured in
1214	>	// angstroms.
1215
1216	<	bool i_is_Charge = data.is_Charge;
1217	<	bool i_is_Dipole = data.is_Dipole;
1218	<
1219	<	if (summationMethod_ == esm_REACTION_FIELD) {
1220	<	if (i_is_Dipole) {
1221	<	mu1 = data.dipole_moment;
1222	<	preVal = pre22_ * preRF2_ * mu1 * mu1;
1223	<	scdat.pot -= 0.5 * preVal;
1216	>	Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
1217	>	Vector3d box = hmat.diagonals();
1218	>	RealType boxMax = box.max();
1219	>
1220	>	//int kMax = int(pow(dampingAlpha_,2)*cutoffRadius_ * boxMax / M_PI);
1221	>	const int kMax = 5;
1222	>	int kSqMax = kMax*kMax + 2;
1223	>
1224	>	int kLimit = kMax+1;
1225	>	int kLim2 = 2*kMax+1;
1226	>	int kSqLim = kSqMax;
1227	>
1228	>	vector<RealType> AK(kSqLim+1, 0.0);
1229	>	RealType xcl = 2.0 * M_PI / box.x();
1230	>	RealType ycl = 2.0 * M_PI / box.y();
1231	>	RealType zcl = 2.0 * M_PI / box.z();
1232	>	RealType rcl = 2.0 * M_PI / boxMax;
1233	>	RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z());
1234	>
1235	>	if(dampingAlpha_ < 1.0e-12) return;
1236	>
1237	>	RealType ralph = -0.25/pow(dampingAlpha_,2);
1238	>
1239	>	// Calculate and store exponential factors
1240	>
1241	>	vector<vector<Vector3d> > eCos;
1242	>	vector<vector<Vector3d> > eSin;
1243	>
1244	>	int nMax = info_->getNAtoms();
1245	>
1246	>	eCos.resize(kLimit+1);
1247	>	eSin.resize(kLimit+1);
1248	>	for (int j = 0; j < kLimit+1; j++) {
1249	>	eCos[j].resize(nMax);
1250	>	eSin[j].resize(nMax);
1251	>	}
1252	>
1253	>	Vector3d t( 2.0 * M_PI );
1254	>	t.Vdiv(t, box);
1255	>
1256	>	SimInfo::MoleculeIterator mi;
1257	>	Molecule::AtomIterator ai;
1258	>	int i;
1259	>	Vector3d r;
1260	>	Vector3d tt;
1261	>	Vector3d w;
1262	>	Vector3d u;
1263	>
1264	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1265	>	mol = info_->nextMolecule(mi)) {
1266	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1267	>	atom = mol->nextAtom(ai)) {
1268
1269	<	// The self-correction term adds into the reaction field vector
1270	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1271	<	Vector3d ei = preVal * uz_i;
1272	<
1273	<	// This looks very wrong.  A vector crossed with itself is zero.
1274	<	scdat.t -= cross(uz_i, ei);
1269	>	i = atom->getLocalIndex();
1270	>	r = atom->getPos();
1271	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r);
1272	>
1273	>	tt.Vmul(t, r);
1274	>
1275	>	eCos[1][i] = Vector3d(1.0, 1.0, 1.0);
1276	>	eSin[1][i] = Vector3d(0.0, 0.0, 0.0);
1277	>	eCos[2][i] = Vector3d(cos(tt.x()), cos(tt.y()), cos(tt.z()));
1278	>	eSin[2][i] = Vector3d(sin(tt.x()), sin(tt.y()), sin(tt.z()));
1279	>	u = 2.0 * eCos[1][i];
1280	>	eCos[3][i].Vmul(u, eCos[2][i]);
1281	>	eSin[3][i].Vmul(u, eSin[2][i]);
1282	>
1283	>	for(int l = 3; l <= kLimit; l++) {
1284	>	w.Vmul(u, eCos[l-1][i]);
1285	>	eCos[l][i] = w - eCos[l-2][i];
1286	>	w.Vmul(u, eSin[l-1][i]);
1287	>	eSin[l][i] = w - eSin[l-2][i];
1288	>	}
1289		}
1290	<	} else if (summationMethod_ == esm_SHIFTED_FORCE || summationMethod_ == esm_SHIFTED_POTENTIAL) {
1291	<	if (i_is_Charge) {
1292	<	chg1 = data.charge;
1293	<	if (screeningMethod_ == DAMPED) {
1294	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1295	<	} else {
1296	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1290	>	}
1291	>
1292	>	// Calculate and store AK coefficients:
1293	>
1294	>	RealType eksq = 1.0;
1295	>	RealType expf = 0.0;
1296	>	if (ralph < 0.0) expf = exp(ralph*rcl*rcl);
1297	>	for (i = 1; i <= kSqLim; i++) {
1298	>	RealType rksq = float(i)*rcl*rcl;
1299	>	eksq = expf*eksq;
1300	>	AK[i] = eConverter * eksq/rksq;
1301	>	}
1302	>
1303	>	/*
1304	>	* Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz)
1305	>	* the values of ll, mm and nn are selected so that the symmetry of
1306	>	* reciprocal lattice is taken into account i.e. the following
1307	>	* rules apply.
1308	>	*
1309	>	* ll ranges over the values 0 to kMax only.
1310	>	*
1311	>	* mm ranges over 0 to kMax when ll=0 and over
1312	>	*            -kMax to kMax otherwise.
1313	>	* nn ranges over 1 to kMax when ll=mm=0 and over
1314	>	*            -kMax to kMax otherwise.
1315	>	*
1316	>	* Hence the result of the summation must be doubled at the end.
1317	>	*/
1318	>
1319	>	std::vector<RealType> clm(nMax, 0.0);
1320	>	std::vector<RealType> slm(nMax, 0.0);
1321	>	std::vector<RealType> ckr(nMax, 0.0);
1322	>	std::vector<RealType> skr(nMax, 0.0);
1323	>	std::vector<RealType> ckc(nMax, 0.0);
1324	>	std::vector<RealType> cks(nMax, 0.0);
1325	>	std::vector<RealType> dkc(nMax, 0.0);
1326	>	std::vector<RealType> dks(nMax, 0.0);
1327	>	std::vector<RealType> qkc(nMax, 0.0);
1328	>	std::vector<RealType> qks(nMax, 0.0);
1329	>	std::vector<Vector3d> dxk(nMax, V3Zero);
1330	>	std::vector<Vector3d> qxk(nMax, V3Zero);
1331	>
1332	>	int mMin = kLimit;
1333	>	int nMin = kLimit + 1;
1334	>	for (int l = 1; l <= kLimit; l++) {
1335	>	int ll =l - 1;
1336	>	RealType rl = xcl * float(ll);
1337	>	for (int mmm = mMin; mmm <= kLim2; mmm++) {
1338	>	int mm = mmm - kLimit;
1339	>	int m = abs(mm) + 1;
1340	>	RealType rm = ycl * float(mm);
1341	>	// Set temporary products of exponential terms
1342	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1343	>	mol = info_->nextMolecule(mi)) {
1344	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1345	>	atom = mol->nextAtom(ai)) {
1346	>
1347	>	i = atom->getLocalIndex();
1348	>	if(mm < 0) {
1349	>	clm[i] = eCos[l][i].x()*eCos[m][i].y()
1350	>	+ eSin[l][i].x()*eSin[m][i].y();
1351	>	slm[i] = eCos[l][i].x()*eCos[m][i].y()
1352	>	- eSin[m][i].y()*eCos[l][i].x();
1353	>	} else {
1354	>	clm[i] = eCos[l][i].x()*eCos[m][i].y()
1355	>	- eSin[l][i].x()*eSin[m][i].y();
1356	>	slm[i] = eSin[l][i].x()*eCos[m][i].y()
1357	>	+ eSin[m][i].y()*eCos[l][i].x();
1358	>	}
1359	>	}
1360		}
1361	<	scdat.pot += self;
1361	>	for (int nnn = nMin; nnn <= kLim2; nnn++) {
1362	>	int nn = nnn - kLimit;
1363	>	int n = abs(nn) + 1;
1364	>	RealType rn = zcl * float(nn);
1365	>	// Test on magnitude of k vector:
1366	>	int kk=ll*ll + mm*mm + nn*nn;
1367	>	if(kk <= kSqLim) {
1368	>	Vector3d kVec = Vector3d(rl, rm, rn);
1369	>	Mat3x3d  k2 = outProduct(kVec, kVec);
1370	>	// Calculate exp(ikr) terms
1371	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1372	>	mol = info_->nextMolecule(mi)) {
1373	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1374	>	atom = mol->nextAtom(ai)) {
1375	>	i = atom->getLocalIndex();
1376	>
1377	>	if (nn < 0) {
1378	>	ckr[i]=clm[i]*eCos[n][i].z()+slm[i]*eSin[n][i].z();
1379	>	skr[i]=slm[i]*eCos[n][i].z()-clm[i]*eSin[n][i].z();
1380	>	} else {
1381	>	ckr[i]=clm[i]*eCos[n][i].z()-slm[i]*eSin[n][i].z();
1382	>	skr[i]=slm[i]*eCos[n][i].z()+clm[i]*eSin[n][i].z();
1383	>	}
1384	>	}
1385	>	}
1386	>
1387	>	// Calculate scalar and vector products for each site:
1388	>
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->getGlobalIndex();
1394	>	int atid = atom->getAtomType()->getIdent();
1395	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]];
1396	>
1397	>	if (data.is_Charge) {
1398	>	RealType C = data.fixedCharge;
1399	>	if (atom->isFluctuatingCharge()) C += atom->getFlucQPos();
1400	>	ckc[i] = C * ckr[i];
1401	>	cks[i] = C * cks[i];
1402	>	}
1403	>
1404	>	if (data.is_Dipole) {
1405	>	Vector3d D = atom->getDipole() * mPoleConverter;
1406	>	RealType dk = dot(kVec, D);
1407	>	dxk[i] = cross(kVec, D);
1408	>	dkc[i] = dk * ckr[i];
1409	>	dks[i] = dk * skr[i];
1410	>	}
1411	>	if (data.is_Quadrupole) {
1412	>	Mat3x3d Q = atom->getQuadrupole();
1413	>	Q *= mPoleConverter;
1414	>	RealType qk = -( Q * k2 ).trace();
1415	>	qxk[i] = -2.0 * cross(k2, Q);
1416	>	qkc[i] = qk * ckr[i];
1417	>	qks[i] = qk * skr[i];
1418	>	}
1419	>	}
1420	>	}
1421	>
1422	>	// calculate vector sums
1423	>
1424	>	RealType ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0);
1425	>	RealType ckss = std::accumulate(cks.begin(),cks.end(),0.0);
1426	>	RealType dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0);
1427	>	RealType dkss = std::accumulate(dks.begin(),dks.end(),0.0);
1428	>	RealType qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0);
1429	>	RealType qkss = std::accumulate(qks.begin(),qks.end(),0.0);
1430	>
1431	>	#ifdef IS_MPI
1432	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckcs, 1, MPI::REALTYPE,
1433	>	MPI::SUM);
1434	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &ckss, 1, MPI::REALTYPE,
1435	>	MPI::SUM);
1436	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkcs, 1, MPI::REALTYPE,
1437	>	MPI::SUM);
1438	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &dkss, 1, MPI::REALTYPE,
1439	>	MPI::SUM);
1440	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkcs, 1, MPI::REALTYPE,
1441	>	MPI::SUM);
1442	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &qkss, 1, MPI::REALTYPE,
1443	>	MPI::SUM);
1444	>	#endif
1445	>
1446	>	// Accumulate potential energy and virial contribution:
1447	>
1448	>	//cerr << "l, m, n = " << l << " " << m << " " << n << "\n";
1449	>	cerr << "kVec = " << kVec << "\n";
1450	>	cerr << "ckss = " << ckss << " ckcs = " << ckcs << "\n";
1451	>	kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss)
1452	>	+ (ckcs-dkss-qkcs)*(ckcs-dkss-qkss));
1453	>	//cerr << "kspace pot = " << kPot << "\n";
1454	>	kVir -= 2.0 * rvol * AK[kk]*(ckcs*ckcs+ckss*ckss
1455	>	+4.0*(ckss*dkcs-ckcs*dkss)
1456	>	+3.0*(dkcs*dkcs+dkss*dkss)
1457	>	-6.0*(ckss*qkss+ckcs*qkcs)
1458	>	+8.0*(dkss*qkcs-dkcs*qkss)
1459	>	+5.0*(qkss*qkss+qkcs*qkcs));
1460	>
1461	>	// Calculate force and torque for each site:
1462	>
1463	>	for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1464	>	mol = info_->nextMolecule(mi)) {
1465	>	for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1466	>	atom = mol->nextAtom(ai)) {
1467	>
1468	>	i = atom->getLocalIndex();
1469	>	int atid = atom->getAtomType()->getIdent();
1470	>	ElectrostaticAtomData data = ElectrostaticMap[Etids[atid]];
1471	>
1472	>	RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs)
1473	>	- (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss));
1474	>	RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs)
1475	>	-ckr[i]*(ckss+dkcs-qkss));
1476	>	RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)+
1477	>	skr[i]*(ckss+dkcs-qkss));
1478	>
1479	>
1480	>	atom->addFrc( 4.0 * rvol * qfrc * kVec );
1481	>
1482	>	if (data.is_Dipole) {
1483	>	atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] );
1484	>	}
1485	>	if (data.is_Quadrupole) {
1486	>	atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] );
1487	>	}
1488	>	}
1489	>	}
1490	>	}
1491	>	}
1492		}
1493		}
1494		}
1068	–
1069	–	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1070	–	// This seems to work moderately well as a default.  There's no
1071	–	// inherent scale for 1/r interactions that we can standardize.
1072	–	// 12 angstroms seems to be a reasonably good guess for most
1073	–	// cases.
1074	–	return 12.0;
1075	–	}
1495		}

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