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root/OpenMD/branches/development/src/nonbonded/Electrostatic.cpp

Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 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).
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).
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>
#	Line 46 | Line 47
47		#include "nonbonded/Electrostatic.hpp"
48		#include "utils/simError.h"
49		#include "types/NonBondedInteractionType.hpp"
50	<	#include "types/DirectionalAtomType.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52	>	#include "types/MultipoleAdapter.hpp"
53		#include "io/Globals.hpp"
54	+	#include "nonbonded/SlaterIntegrals.hpp"
55	+	#include "utils/PhysicalConstants.hpp"
56	+	#include "math/erfc.hpp"
57	+	#include "math/SquareMatrix.hpp"
58
59		namespace OpenMD {
60
61		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
62	<	forceField_(NULL) {}
62	>	forceField_(NULL), info_(NULL),
63	>	haveCutoffRadius_(false),
64	>	haveDampingAlpha_(false),
65	>	haveDielectric_(false),
66	>	haveElectroSplines_(false)
67	>	{}
68
69		void Electrostatic::initialize() {
70	+
71	+	Globals* simParams_ = info_->getSimParams();
72
59	–	Globals* simParams_;
60	–
73		summationMap_["HARD"]               = esm_HARD;
74	+	summationMap_["NONE"]               = esm_HARD;
75		summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
76		summationMap_["SHIFTED_POTENTIAL"]  = esm_SHIFTED_POTENTIAL;
77		summationMap_["SHIFTED_FORCE"]      = esm_SHIFTED_FORCE;
#	Line 76 | Line 89 | namespace OpenMD {
89		// Charge-Dipole, assuming charges are measured in electrons, and
90		// dipoles are measured in debyes
91		pre12_ = 69.13373;
92	<	// Dipole-Dipole, assuming dipoles are measured in debyes
92	>	// Dipole-Dipole, assuming dipoles are measured in Debye
93		pre22_ = 14.39325;
94		// Charge-Quadrupole, assuming charges are measured in electrons, and
95		// quadrupoles are measured in 10^-26 esu cm^2
96	<	// This unit is also known affectionately as an esu centi-barn.
96	>	// This unit is also known affectionately as an esu centibarn.
97		pre14_ = 69.13373;
98	<
98	>	// Dipole-Quadrupole, assuming dipoles are measured in debyes and
99	>	// quadrupoles in esu centibarns:
100	>	pre24_ = 14.39325;
101	>	// Quadrupole-Quadrupole, assuming esu centibarns:
102	>	pre44_ = 14.39325;
103	>
104		// conversions for the simulation box dipole moment
105		chargeToC_ = 1.60217733e-19;
106		angstromToM_ = 1.0e-10;
#	Line 96 | Line 114 | namespace OpenMD {
114		summationMethod_ = esm_HARD;
115		screeningMethod_ = UNDAMPED;
116		dielectric_ = 1.0;
99	–	one_third_ = 1.0 / 3.0;
100	–	haveCutoffRadius_ = false;
101	–	haveDampingAlpha_ = false;
102	–	haveDielectric_ = false;
103	–	haveElectroSpline_ = false;
117
118		// check the summation method:
119		if (simParams_->haveElectrostaticSummationMethod()) {
#	Line 113 | Line 126 | namespace OpenMD {
126		} else {
127		// throw error
128		sprintf( painCave.errMsg,
129	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
129	>	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
130		"\t(Input file specified %s .)\n"
131	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
131	>	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
132		"\t\"shifted_potential\", \"shifted_force\", or \n"
133		"\t\"reaction_field\".\n", myMethod.c_str() );
134		painCave.isFatal = 1;
#	Line 185 | Line 198 | namespace OpenMD {
198
199		// throw warning
200		sprintf( painCave.errMsg,
201	<	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
202	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
201	>	"Electrostatic::initialize: dampingAlpha was not specified in the\n"
202	>	"\tinput file.  A default value of %f (1/ang) will be used for the\n"
203	>	"\tcutoff of %f (ang).\n",
204		dampingAlpha_, cutoffRadius_);
205		painCave.severity = OPENMD_INFO;
206		painCave.isFatal = 0;
#	Line 207 | Line 221 | namespace OpenMD {
221
222		if (at->isElectrostatic())
223		addType(at);
224	<	}
224	>	}
225
212	–
213	–	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
214	–	rcuti_ = 1.0 / cutoffRadius_;
215	–	rcuti2_ = rcuti_ * rcuti_;
216	–	rcuti3_ = rcuti2_ * rcuti_;
217	–	rcuti4_ = rcuti2_ * rcuti2_;
218	–
219	–	if (screeningMethod_ == DAMPED) {
220	–
221	–	alpha2_ = dampingAlpha_ * dampingAlpha_;
222	–	alpha4_ = alpha2_ * alpha2_;
223	–	alpha6_ = alpha4_ * alpha2_;
224	–	alpha8_ = alpha4_ * alpha4_;
225	–
226	–	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
227	–	invRootPi_ = 0.56418958354775628695;
228	–	alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
229	–
230	–	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
231	–	c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
232	–	c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
233	–	c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
234	–	c5c_ = 8.0 * alphaPi_ * alpha6_ + 7.0 * c4c_ * rcuti2_;
235	–	c6c_ = 16.0 * alphaPi_ * alpha8_ + 9.0 * c5c_ * rcuti2_;
236	–	} else {
237	–	c1c_ = rcuti_;
238	–	c2c_ = c1c_ * rcuti_;
239	–	c3c_ = 3.0 * c2c_ * rcuti_;
240	–	c4c_ = 5.0 * c3c_ * rcuti2_;
241	–	c5c_ = 7.0 * c4c_ * rcuti2_;
242	–	c6c_ = 9.0 * c5c_ * rcuti2_;
243	–	}
244	–
226		if (summationMethod_ == esm_REACTION_FIELD) {
227		preRF_ = (dielectric_ - 1.0) /
228	<	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
248	<	preRF2_ = 2.0 * preRF_;
228	>	((2.0 * dielectric_ + 1.0) * pow(cutoffRadius_,3) );
229		}
230
231	<	RealType dx = cutoffRadius_ / RealType(np_ - 1);
232	<	RealType rval;
233	<	vector<RealType> rvals;
234	<	vector<RealType> yvals;
235	<	for (int i = 0; i < np_; i++) {
236	<	rval = RealType(i) * dx;
257	<	rvals.push_back(rval);
258	<	yvals.push_back(erfc(dampingAlpha_ * rval));
259	<	}
260	<	erfcSpline_ = new CubicSpline();
261	<	erfcSpline_->addPoints(rvals, yvals);
262	<	haveElectroSpline_ = true;
231	>	RealType b0c, b1c, b2c, b3c, b4c, b5c;
232	>	RealType db0c_1, db0c_2, db0c_3, db0c_4, db0c_5;
233	>	RealType a2, expTerm, invArootPi;
234	>
235	>	RealType r = cutoffRadius_;
236	>	RealType r2 = r * r;
237
238	<	initialized_ = true;
239	<	}
240	<
241	<	void Electrostatic::addType(AtomType* atomType){
238	>	if (screeningMethod_ == DAMPED) {
239	>	a2 = dampingAlpha_ * dampingAlpha_;
240	>	invArootPi = 1.0 / (dampingAlpha_ * sqrt(M_PI));
241	>	expTerm = exp(-a2 * r2);
242	>	// values of Smith's B_l functions at the cutoff radius:
243	>	b0c = erfc(dampingAlpha_ * r) / r;
244	>	b1c = (      b0c     + 2.0*a2     * expTerm * invArootPi) / r2;
245	>	b2c = (3.0 * b1c + pow(2.0*a2, 2) * expTerm * invArootPi) / r2;
246	>	b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2;
247	>	b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2;
248	>	b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2;
249	>	selfMult_ = b0c  +  2.0 * a2 * invArootPi;
250	>	} else {
251	>	a2 = 0.0;
252	>	b0c = 1.0 / r;
253	>	b1c = (      b0c) / r2;
254	>	b2c = (3.0 * b1c) / r2;
255	>	b3c = (5.0 * b2c) / r2;
256	>	b4c = (7.0 * b3c) / r2;
257	>	b5c = (9.0 * b4c) / r2;
258	>	selfMult_ = b0c;
259	>	}
260
261	<	ElectrostaticAtomData electrostaticAtomData;
262	<	electrostaticAtomData.is_Charge = false;
263	<	electrostaticAtomData.is_Dipole = false;
264	<	electrostaticAtomData.is_SplitDipole = false;
265	<	electrostaticAtomData.is_Quadrupole = false;
261	>	// higher derivatives of B_0 at the cutoff radius:
262	>	db0c_1 = -r * b1c;
263	>	db0c_2 =     -b1c + r2 * b2c;
264	>	db0c_3 =          3.0*r*b2c  - r2*r*b3c;
265	>	db0c_4 =          3.0*b2c  - 6.0*r2*b3c     + r2*r2*b4c;
266	>	db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;
267	>
268	>	// working variables for the splines:
269	>	RealType ri, ri2;
270	>	RealType b0, b1, b2, b3, b4, b5;
271	>	RealType db0_1, db0_2, db0_3, db0_4, db0_5;
272	>	RealType f0;
273	>	RealType g0, g1, g2, g3, g4;
274	>	RealType h1, h2, h3, h4;
275	>	RealType s2, s3, s4;
276	>	RealType t3, t4;
277	>	RealType u4;
278
279	<	if (atomType->isCharge()) {
280	<	GenericData* data = atomType->getPropertyByName("Charge");
279	>	// working variables for Taylor expansion:
280	>	RealType rmRc, rmRc2, rmRc3, rmRc4;
281
282	<	if (data == NULL) {
283	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
284	<	"Charge\n"
285	<	"\tparameters for atomType %s.\n",
286	<	atomType->getName().c_str());
283	<	painCave.severity = OPENMD_ERROR;
284	<	painCave.isFatal = 1;
285	<	simError();
286	<	}
287	<
288	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
289	<	if (doubleData == NULL) {
290	<	sprintf( painCave.errMsg,
291	<	"Electrostatic::addType could not convert GenericData to "
292	<	"Charge for\n"
293	<	"\tatom type %s\n", atomType->getName().c_str());
294	<	painCave.severity = OPENMD_ERROR;
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<	electrostaticAtomData.is_Charge = true;
299	<	electrostaticAtomData.charge = doubleData->getData();
300	<	}
282	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
283	>	// have charged atoms longer than the cutoffRadius away from each
284	>	// other.  Splining is almost certainly the best choice here.
285	>	// Direct calls to erfc would be preferrable if it is a very fast
286	>	// implementation.
287
288	<	if (atomType->isDirectional()) {
289	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
290	<
291	<	if (daType->isDipole()) {
292	<	GenericData* data = daType->getPropertyByName("Dipole");
293	<
294	<	if (data == NULL) {
295	<	sprintf( painCave.errMsg,
296	<	"Electrostatic::addType could not find Dipole\n"
297	<	"\tparameters for atomType %s.\n",
298	<	daType->getName().c_str());
299	<	painCave.severity = OPENMD_ERROR;
300	<	painCave.isFatal = 1;
301	<	simError();
302	<	}
303	<
304	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
305	<	if (doubleData == NULL) {
306	<	sprintf( painCave.errMsg,
307	<	"Electrostatic::addType could not convert GenericData to "
308	<	"Dipole Moment\n"
309	<	"\tfor atom type %s\n", daType->getName().c_str());
310	<	painCave.severity = OPENMD_ERROR;
311	<	painCave.isFatal = 1;
312	<	simError();
313	<	}
314	<	electrostaticAtomData.is_Dipole = true;
315	<	electrostaticAtomData.dipole_moment = doubleData->getData();
288	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_);
289	>
290	>	// Storage vectors for the computed functions
291	>	vector<RealType> rv;
292	>	vector<RealType> v01v, v02v;
293	>	vector<RealType> v11v, v12v, v13v;
294	>	vector<RealType> v21v, v22v, v23v, v24v;
295	>	vector<RealType> v31v, v32v, v33v, v34v, v35v;
296	>	vector<RealType> v41v, v42v, v43v, v44v, v45v, v46v;
297	>
298	>	for (int i = 1; i < np_ + 1; i++) {
299	>	r = RealType(i) * dx;
300	>	rv.push_back(r);
301	>
302	>	ri = 1.0 / r;
303	>	ri2 = ri * ri;
304	>
305	>	r2 = r * r;
306	>	expTerm = exp(-a2 * r2);
307	>
308	>	// Taylor expansion factors (no need for factorials this way):
309	>	rmRc = r - cutoffRadius_;
310	>	rmRc2 = rmRc  * rmRc / 2.0;
311	>	rmRc3 = rmRc2 * rmRc / 3.0;
312	>	rmRc4 = rmRc3 * rmRc / 4.0;
313	>
314	>	// values of Smith's B_l functions at r:
315	>	if (screeningMethod_ == DAMPED) {
316	>	b0 = erfc(dampingAlpha_ * r) * ri;
317	>	b1 = (      b0 +     2.0*a2     * expTerm * invArootPi) * ri2;
318	>	b2 = (3.0 * b1 + pow(2.0*a2, 2) * expTerm * invArootPi) * ri2;
319	>	b3 = (5.0 * b2 + pow(2.0*a2, 3) * expTerm * invArootPi) * ri2;
320	>	b4 = (7.0 * b3 + pow(2.0*a2, 4) * expTerm * invArootPi) * ri2;
321	>	b5 = (9.0 * b4 + pow(2.0*a2, 5) * expTerm * invArootPi) * ri2;
322	>	} else {
323	>	b0 = ri;
324	>	b1 = (      b0) * ri2;
325	>	b2 = (3.0 * b1) * ri2;
326	>	b3 = (5.0 * b2) * ri2;
327	>	b4 = (7.0 * b3) * ri2;
328	>	b5 = (9.0 * b4) * ri2;
329		}
330	+
331	+	// higher derivatives of B_0 at r:
332	+	db0_1 = -r * b1;
333	+	db0_2 =     -b1 + r2 * b2;
334	+	db0_3 =          3.0*r*b2   - r2*r*b3;
335	+	db0_4 =          3.0*b2   - 6.0*r2*b3     + r2*r2*b4;
336	+	db0_5 =                    -15.0*r*b3 + 10.0*r2*r*b4 - r2*r2*r*b5;
337
338	<	if (daType->isSplitDipole()) {
339	<	GenericData* data = daType->getPropertyByName("SplitDipoleDistance");
338	>
339	>	switch (summationMethod_) {
340	>	case esm_SHIFTED_FORCE:
341	>	f0 = b0 - b0c - rmRc*db0c_1;
342
343	<	if (data == NULL) {
344	<	sprintf(painCave.errMsg,
345	<	"Electrostatic::addType could not find SplitDipoleDistance\n"
346	<	"\tparameter for atomType %s.\n",
347	<	daType->getName().c_str());
348	<	painCave.severity = OPENMD_ERROR;
349	<	painCave.isFatal = 1;
350	<	simError();
351	<	}
352	<
353	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
354	<	if (doubleData == NULL) {
355	<	sprintf( painCave.errMsg,
356	<	"Electrostatic::addType could not convert GenericData to "
357	<	"SplitDipoleDistance for\n"
358	<	"\tatom type %s\n", daType->getName().c_str());
359	<	painCave.severity = OPENMD_ERROR;
360	<	painCave.isFatal = 1;
361	<	simError();
362	<	}
355	<	electrostaticAtomData.is_SplitDipole = true;
356	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
357	<	}
343	>	g0 = db0_1 - db0c_1;
344	>	g1 = g0 - rmRc *db0c_2;
345	>	g2 = g1 - rmRc2*db0c_3;
346	>	g3 = g2 - rmRc3*db0c_4;
347	>	g4 = g3 - rmRc4*db0c_5;
348	>
349	>	h1 = db0_2 - db0c_2;
350	>	h2 = h1 - rmRc *db0c_3;
351	>	h3 = h2 - rmRc2*db0c_4;
352	>	h4 = h3 - rmRc3*db0c_5;
353	>
354	>	s2 = db0_3 - db0c_3;
355	>	s3 = s2 - rmRc *db0c_4;
356	>	s4 = s3 - rmRc2*db0c_5;
357	>
358	>	t3 = db0_4 - db0c_4;
359	>	t4 = t3 - rmRc *db0c_5;
360	>
361	>	u4 = db0_5 - db0c_5;
362	>	break;
363
364	<	if (daType->isQuadrupole()) {
365	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
364	>	case esm_SHIFTED_POTENTIAL:
365	>	f0 = b0 - b0c;
366
367	<	if (data == NULL) {
368	<	sprintf( painCave.errMsg,
369	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
370	<	"\tparameter for atomType %s.\n",
371	<	daType->getName().c_str());
372	<	painCave.severity = OPENMD_ERROR;
373	<	painCave.isFatal = 1;
374	<	simError();
375	<	}
367	>	g0 = db0_1;
368	>	g1 = db0_1 - db0c_1;
369	>	g2 = g1 - rmRc *db0c_2;
370	>	g3 = g2 - rmRc2*db0c_3;
371	>	g4 = g3 - rmRc3*db0c_4;
372	>
373	>	h1 = db0_2;
374	>	h2 = db0_2 - db0c_2;
375	>	h3 = h2 - rmRc *db0c_3;
376	>	h4 = h3 - rmRc2*db0c_4;
377
378	<	// Quadrupoles in OpenMD are set as the diagonal elements
379	<	// of the diagonalized traceless quadrupole moment tensor.
380	<	// The column vectors of the unitary matrix that diagonalizes
375	<	// the quadrupole moment tensor become the eFrame (or the
376	<	// electrostatic version of the body-fixed frame.
378	>	s2 = db0_3;
379	>	s3 = db0_3 - db0c_3;
380	>	s4 = s3 - rmRc *db0c_4;
381
382	<	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
383	<	if (v3dData == NULL) {
384	<	sprintf( painCave.errMsg,
385	<	"Electrostatic::addType could not convert GenericData to "
386	<	"Quadrupole Moments for\n"
387	<	"\tatom type %s\n", daType->getName().c_str());
388	<	painCave.severity = OPENMD_ERROR;
389	<	painCave.isFatal = 1;
390	<	simError();
382	>	t3 = db0_4;
383	>	t4 = db0_4 - db0c_4;
384	>
385	>	u4 = db0_5;
386	>	break;
387	>
388	>	case esm_SWITCHING_FUNCTION:
389	>	case esm_HARD:
390	>	f0 = b0;
391	>
392	>	g0 = db0_1;
393	>	g1 = g0;
394	>	g2 = g1;
395	>	g3 = g2;
396	>	g4 = g3;
397	>
398	>	h1 = db0_2;
399	>	h2 = h1;
400	>	h3 = h2;
401	>	h4 = h3;
402	>
403	>	s2 = db0_3;
404	>	s3 = s2;
405	>	s4 = s3;
406	>
407	>	t3 = db0_4;
408	>	t4 = t3;
409	>
410	>	u4 = db0_5;
411	>	break;
412	>
413	>	case esm_REACTION_FIELD:
414	>
415	>	// following DL_POLY's lead for shifting the image charge potential:
416	>	f0 = b0  + preRF_ * r2
417	>	- (b0c + preRF_ * cutoffRadius_ * cutoffRadius_);
418	>
419	>	g0 = db0_1 + preRF_ * 2.0 * r;
420	>	g1 = g0;
421	>	g2 = g1;
422	>	g3 = g2;
423	>	g4 = g3;
424	>
425	>	h1 = db0_2 + preRF_ * 2.0;
426	>	h2 = h1;
427	>	h3 = h2;
428	>	h4 = h3;
429	>
430	>	s2 = db0_3;
431	>	s3 = s2;
432	>	s4 = s3;
433	>
434	>	t3 = db0_4;
435	>	t4 = t3;
436	>
437	>	u4 = db0_5;
438	>	break;
439	>
440	>	case esm_EWALD_FULL:
441	>	case esm_EWALD_PME:
442	>	case esm_EWALD_SPME:
443	>	default :
444	>	map<string, ElectrostaticSummationMethod>::iterator i;
445	>	std::string meth;
446	>	for (i = summationMap_.begin(); i != summationMap_.end(); ++i) {
447	>	if ((*i).second == summationMethod_) meth = (*i).first;
448		}
449	+	sprintf( painCave.errMsg,
450	+	"Electrostatic::initialize: electrostaticSummationMethod %s \n"
451	+	"\thas not been implemented yet. Please select one of:\n"
452	+	"\t\"hard\", \"shifted_potential\", or \"shifted_force\"\n",
453	+	meth.c_str() );
454	+	painCave.isFatal = 1;
455	+	simError();
456	+	break;
457	+	}
458	+
459	+	v01 = f0;
460	+	v02 = g0;
461	+
462	+	v11 = g1;
463	+	v12 = g1 * ri;
464	+	v13 = h1 - v12;
465	+
466	+	v21 = g2 * ri;
467	+	v22 = h2 - v21;
468	+	v23 = v22 * ri;
469	+	v24 = s2 - 3.0*v23;
470	+
471	+	v31 = (h3 - g3 * ri) * ri;
472	+	v32 = s3 - 3.0*v31;
473	+	v33 = v31 * ri;
474	+	v34 = v32 * ri;
475	+	v35 = t3 - 6.0*v34 - 3.0*v33;
476	+
477	+	v41 = (h4 - g4 * ri) * ri2;
478	+	v42 = s4 * ri - 3.0*v41;
479	+	v43 = t4 - 6.0*v42 - 3.0*v41;
480	+	v44 = v42 * ri;
481	+	v45 = v43 * ri;
482	+	v46 = u4 - 10.0*v45 - 15.0*v44;
483	+
484	+	// Add these computed values to the storage vectors for spline creation:
485	+	v01v.push_back(v01);
486	+	v02v.push_back(v02);
487	+
488	+	v11v.push_back(v11);
489	+	v12v.push_back(v12);
490	+	v13v.push_back(v13);
491	+
492	+	v21v.push_back(v21);
493	+	v22v.push_back(v22);
494	+	v23v.push_back(v23);
495	+	v24v.push_back(v24);
496	+
497	+	v31v.push_back(v31);
498	+	v32v.push_back(v32);
499	+	v33v.push_back(v33);
500	+	v34v.push_back(v34);
501	+	v35v.push_back(v35);
502	+
503	+	v41v.push_back(v41);
504	+	v42v.push_back(v42);
505	+	v43v.push_back(v43);
506	+	v44v.push_back(v44);
507	+	v45v.push_back(v45);
508	+	v46v.push_back(v46);
509	+	}
510	+
511	+	// construct the spline structures and fill them with the values we've
512	+	// computed:
513	+
514	+	v01s = new CubicSpline();
515	+	v01s->addPoints(rv, v01v);
516	+	v02s = new CubicSpline();
517	+	v02s->addPoints(rv, v02v);
518	+
519	+	v11s = new CubicSpline();
520	+	v11s->addPoints(rv, v11v);
521	+	v12s = new CubicSpline();
522	+	v12s->addPoints(rv, v12v);
523	+	v13s = new CubicSpline();
524	+	v13s->addPoints(rv, v13v);
525	+
526	+	v21s = new CubicSpline();
527	+	v21s->addPoints(rv, v21v);
528	+	v22s = new CubicSpline();
529	+	v22s->addPoints(rv, v22v);
530	+	v23s = new CubicSpline();
531	+	v23s->addPoints(rv, v23v);
532	+	v24s = new CubicSpline();
533	+	v24s->addPoints(rv, v24v);
534	+
535	+	v31s = new CubicSpline();
536	+	v31s->addPoints(rv, v31v);
537	+	v32s = new CubicSpline();
538	+	v32s->addPoints(rv, v32v);
539	+	v33s = new CubicSpline();
540	+	v33s->addPoints(rv, v33v);
541	+	v34s = new CubicSpline();
542	+	v34s->addPoints(rv, v34v);
543	+	v35s = new CubicSpline();
544	+	v35s->addPoints(rv, v35v);
545	+
546	+	v41s = new CubicSpline();
547	+	v41s->addPoints(rv, v41v);
548	+	v42s = new CubicSpline();
549	+	v42s->addPoints(rv, v42v);
550	+	v43s = new CubicSpline();
551	+	v43s->addPoints(rv, v43v);
552	+	v44s = new CubicSpline();
553	+	v44s->addPoints(rv, v44v);
554	+	v45s = new CubicSpline();
555	+	v45s->addPoints(rv, v45v);
556	+	v46s = new CubicSpline();
557	+	v46s->addPoints(rv, v46v);
558	+
559	+	haveElectroSplines_ = true;
560	+
561	+	initialized_ = true;
562	+	}
563	+
564	+	void Electrostatic::addType(AtomType* atomType){
565	+
566	+	ElectrostaticAtomData electrostaticAtomData;
567	+	electrostaticAtomData.is_Charge = false;
568	+	electrostaticAtomData.is_Dipole = false;
569	+	electrostaticAtomData.is_Quadrupole = false;
570	+	electrostaticAtomData.is_Fluctuating = false;
571	+
572	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
573	+
574	+	if (fca.isFixedCharge()) {
575	+	electrostaticAtomData.is_Charge = true;
576	+	electrostaticAtomData.fixedCharge = fca.getCharge();
577	+	}
578	+
579	+	MultipoleAdapter ma = MultipoleAdapter(atomType);
580	+	if (ma.isMultipole()) {
581	+	if (ma.isDipole()) {
582	+	electrostaticAtomData.is_Dipole = true;
583	+	electrostaticAtomData.dipole = ma.getDipole();
584	+	}
585	+	if (ma.isQuadrupole()) {
586		electrostaticAtomData.is_Quadrupole = true;
587	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
587	>	electrostaticAtomData.quadrupole = ma.getQuadrupole();
588		}
589		}
590
591	<	AtomTypeProperties atp = atomType->getATP();
591	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
592
593	+	if (fqa.isFluctuatingCharge()) {
594	+	electrostaticAtomData.is_Fluctuating = true;
595	+	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
596	+	electrostaticAtomData.hardness = fqa.getHardness();
597	+	electrostaticAtomData.slaterN = fqa.getSlaterN();
598	+	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
599	+	}
600	+
601		pair<map<int,AtomType*>::iterator,bool> ret;
602	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
602	>	ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
603	>	atomType) );
604		if (ret.second == false) {
605		sprintf( painCave.errMsg,
606		"Electrostatic already had a previous entry with ident %d\n",
607	<	atp.ident);
607	>	atomType->getIdent() );
608		painCave.severity = OPENMD_INFO;
609		painCave.isFatal = 0;
610		simError();
611		}
612
613	<	ElectrostaticMap[atomType] = electrostaticAtomData;
613	>	ElectrostaticMap[atomType] = electrostaticAtomData;
614	>
615	>	// Now, iterate over all known types and add to the mixing map:
616	>
617	>	map<AtomType*, ElectrostaticAtomData>::iterator it;
618	>	for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
619	>	AtomType* atype2 = (*it).first;
620	>	ElectrostaticAtomData eaData2 = (*it).second;
621	>	if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) {
622	>
623	>	RealType a = electrostaticAtomData.slaterZeta;
624	>	RealType b = eaData2.slaterZeta;
625	>	int m = electrostaticAtomData.slaterN;
626	>	int n = eaData2.slaterN;
627	>
628	>	// Create the spline of the coulombic integral for s-type
629	>	// Slater orbitals.  Add a 2 angstrom safety window to deal
630	>	// with cutoffGroups that have charged atoms longer than the
631	>	// cutoffRadius away from each other.
632	>
633	>	RealType rval;
634	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
635	>	vector<RealType> rvals;
636	>	vector<RealType> Jvals;
637	>	// don't start at i = 0, as rval = 0 is undefined for the
638	>	// slater overlap integrals.
639	>	for (int i = 1; i < np_+1; i++) {
640	>	rval = RealType(i) * dr;
641	>	rvals.push_back(rval);
642	>	Jvals.push_back(sSTOCoulInt( a, b, m, n, rval *
643	>	PhysicalConstants::angstromToBohr ) *
644	>	PhysicalConstants::hartreeToKcal );
645	>	}
646	>
647	>	CubicSpline* J = new CubicSpline();
648	>	J->addPoints(rvals, Jvals);
649	>
650	>	pair<AtomType*, AtomType*> key1, key2;
651	>	key1 = make_pair(atomType, atype2);
652	>	key2 = make_pair(atype2, atomType);
653	>
654	>	Jij[key1] = J;
655	>	Jij[key2] = J;
656	>	}
657	>	}
658	>
659		return;
660		}
661
662	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
663	<	RealType theRSW ) {
412	<	cutoffRadius_ = theECR;
413	<	rrf_ = cutoffRadius_;
414	<	rt_ = theRSW;
662	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
663	>	cutoffRadius_ = rCut;
664		haveCutoffRadius_ = true;
665		}
666	+
667		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
668		summationMethod_ = esm;
669		}
#	Line 429 | Line 679 | namespace OpenMD {
679		haveDielectric_ = true;
680		}
681
682	<	void Electrostatic::calcForce(InteractionData idat) {
682	>	void Electrostatic::calcForce(InteractionData &idat) {
683
684	<	// utility variables.  Should clean these up and use the Vector3d and
685	<	// Mat3x3d to replace as many as we can in future versions:
684	>	RealType C_a, C_b;  // Charges
685	>	Vector3d D_a, D_b;  // Dipoles (space-fixed)
686	>	Mat3x3d  Q_a, Q_b;  // Quadrupoles (space-fixed)
687
688	<	RealType q_i, q_j, mu_i, mu_j, d_i, d_j;
689	<	RealType qxx_i, qyy_i, qzz_i;
690	<	RealType qxx_j, qyy_j, qzz_j;
691	<	RealType cx_i, cy_i, cz_i;
692	<	RealType cx_j, cy_j, cz_j;
693	<	RealType cx2, cy2, cz2;
443	<	RealType ct_i, ct_j, ct_ij, a1;
444	<	RealType riji, ri, ri2, ri3, ri4;
445	<	RealType pref, vterm, epot, dudr;
446	<	RealType scale, sc2;
447	<	RealType pot_term, preVal, rfVal;
448	<	RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
449	<	RealType preSw, preSwSc;
450	<	RealType c1, c2, c3, c4;
451	<	RealType erfcVal, derfcVal;
452	<	RealType BigR;
688	>	RealType ri, ri2, ri3, ri4;                  // Distance utility scalars
689	>	RealType rdDa, rdDb;                         // Dipole utility scalars
690	>	Vector3d rxDa, rxDb;                         // Dipole utility vectors
691	>	RealType rdQar, rdQbr, trQa, trQb;           // Quadrupole utility scalars
692	>	Vector3d Qar, Qbr, rQa, rQb, rxQar, rxQbr;   // Quadrupole utility vectors
693	>	RealType pref;
694
695	<	Vector3d Q_i, Q_j;
696	<	Vector3d ux_i, uy_i, uz_i;
697	<	Vector3d ux_j, uy_j, uz_j;
698	<	Vector3d dudux_i, duduy_i, duduz_i;
458	<	Vector3d dudux_j, duduy_j, duduz_j;
459	<	Vector3d rhatdot2, rhatc4;
460	<	Vector3d dVdr;
695	>	RealType DadDb, trQaQb, DadQbr, DbdQar;       // Cross-interaction scalars
696	>	Vector3d DaxDb, DadQb, DbdQa, DaxQbr, DbxQar; // Cross-interaction vectors
697	>	Vector3d rQaQb, QaQbr, QaxQb;
698	>	Mat3x3d  QaQb;                                // Cross-interaction matrices
699
700	<	pair<RealType, RealType> res;
700	>	RealType U(0.0);  // Potential
701	>	Vector3d F(0.0);  // Force
702	>	Vector3d Ta(0.0); // Torque on site a
703	>	Vector3d Tb(0.0); // Torque on site b
704	>	Vector3d Ea(0.0); // Electric field at site a
705	>	Vector3d Eb(0.0); // Electric field at site b
706	>	RealType dUdCa(0.0); // fluctuating charge force at site a
707	>	RealType dUdCb(0.0); // fluctuating charge force at site a
708
709	+	// Indirect interactions mediated by the reaction field.
710	+	RealType indirect_Pot(0.0);  // Potential
711	+	Vector3d indirect_F(0.0);    // Force
712	+	Vector3d indirect_Ta(0.0);   // Torque on site a
713	+	Vector3d indirect_Tb(0.0);   // Torque on site b
714	+
715	+	// Excluded potential that is still computed for fluctuating charges
716	+	RealType excluded_Pot(0.0);
717	+
718	+	RealType rfContrib, coulInt;
719	+
720	+	// spline for coulomb integral
721	+	CubicSpline* J;
722	+
723		if (!initialized_) initialize();
724
725	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
726	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
725	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
726	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
727
728		// some variables we'll need independent of electrostatic type:
729
730	<	riji = 1.0 / idat.rij;
731	<	Vector3d rhat = idat.d  * riji;
732	<
730	>	ri = 1.0 /  *(idat.rij);
731	>	Vector3d rhat =  *(idat.d)  * ri;
732	>	ri2 = ri * ri;
733	>
734		// logicals
735
736	<	bool i_is_Charge = data1.is_Charge;
737	<	bool i_is_Dipole = data1.is_Dipole;
738	<	bool i_is_SplitDipole = data1.is_SplitDipole;
739	<	bool i_is_Quadrupole = data1.is_Quadrupole;
736	>	bool a_is_Charge = data1.is_Charge;
737	>	bool a_is_Dipole = data1.is_Dipole;
738	>	bool a_is_Quadrupole = data1.is_Quadrupole;
739	>	bool a_is_Fluctuating = data1.is_Fluctuating;
740
741	<	bool j_is_Charge = data2.is_Charge;
742	<	bool j_is_Dipole = data2.is_Dipole;
743	<	bool j_is_SplitDipole = data2.is_SplitDipole;
744	<	bool j_is_Quadrupole = data2.is_Quadrupole;
485	<
486	<	if (i_is_Charge)
487	<	q_i = data1.charge;
741	>	bool b_is_Charge = data2.is_Charge;
742	>	bool b_is_Dipole = data2.is_Dipole;
743	>	bool b_is_Quadrupole = data2.is_Quadrupole;
744	>	bool b_is_Fluctuating = data2.is_Fluctuating;
745
746	<	if (i_is_Dipole) {
747	<	mu_i = data1.dipole_moment;
491	<	uz_i = idat.eFrame1.getColumn(2);
492	<
493	<	ct_i = dot(uz_i, rhat);
494	<
495	<	if (i_is_SplitDipole)
496	<	d_i = data1.split_dipole_distance;
497	<
498	<	duduz_i = V3Zero;
499	<	}
746	>	// Obtain all of the required radial function values from the
747	>	// spline structures:
748
749	<	if (i_is_Quadrupole) {
750	<	Q_i = data1.quadrupole_moments;
751	<	qxx_i = Q_i.x();
504	<	qyy_i = Q_i.y();
505	<	qzz_i = Q_i.z();
506	<
507	<	ux_i = idat.eFrame1.getColumn(0);
508	<	uy_i = idat.eFrame1.getColumn(1);
509	<	uz_i = idat.eFrame1.getColumn(2);
510	<
511	<	cx_i = dot(ux_i, rhat);
512	<	cy_i = dot(uy_i, rhat);
513	<	cz_i = dot(uz_i, rhat);
514	<
515	<	dudux_i = V3Zero;
516	<	duduy_i = V3Zero;
517	<	duduz_i = V3Zero;
749	>	if (a_is_Charge && b_is_Charge) {
750	>	v01 = v01s->getValueAt( *(idat.rij) );
751	>	v02 = v02s->getValueAt( *(idat.rij) );
752		}
753	+	if ((a_is_Charge && b_is_Dipole) || (b_is_Charge && a_is_Dipole)) {
754	+	v11 = v11s->getValueAt( *(idat.rij) );
755	+	v12 = v12s->getValueAt( *(idat.rij) );
756	+	v13 = v13s->getValueAt( *(idat.rij) );
757	+	}
758	+	if ((a_is_Charge && b_is_Quadrupole) ||
759	+	(b_is_Charge && a_is_Quadrupole) ||
760	+	(a_is_Dipole && b_is_Dipole)) {
761	+	v21 = v21s->getValueAt( *(idat.rij) );
762	+	v22 = v22s->getValueAt( *(idat.rij) );
763	+	v23 = v23s->getValueAt( *(idat.rij) );
764	+	v24 = v24s->getValueAt( *(idat.rij) );
765	+	}
766	+	if ((a_is_Dipole && b_is_Quadrupole) ||
767	+	(b_is_Dipole && a_is_Quadrupole)) {
768	+	v31 = v31s->getValueAt( *(idat.rij) );
769	+	v32 = v32s->getValueAt( *(idat.rij) );
770	+	v33 = v33s->getValueAt( *(idat.rij) );
771	+	v34 = v34s->getValueAt( *(idat.rij) );
772	+	v35 = v35s->getValueAt( *(idat.rij) );
773	+	}
774	+	if (a_is_Quadrupole && b_is_Quadrupole) {
775	+	v41 = v41s->getValueAt( *(idat.rij) );
776	+	v42 = v42s->getValueAt( *(idat.rij) );
777	+	v43 = v43s->getValueAt( *(idat.rij) );
778	+	v44 = v44s->getValueAt( *(idat.rij) );
779	+	v45 = v45s->getValueAt( *(idat.rij) );
780	+	v46 = v46s->getValueAt( *(idat.rij) );
781	+	}
782
520	–	if (j_is_Charge)
521	–	q_j = data2.charge;
783
784	<	if (j_is_Dipole) {
785	<	mu_j = data2.dipole_moment;
786	<	uz_j = idat.eFrame2.getColumn(2);
784	>	// calculate the single-site contributions (fields, etc).
785	>
786	>	if (a_is_Charge) {
787	>	C_a = data1.fixedCharge;
788
789	<	ct_j = dot(uz_j, rhat);
790	<
791	<	if (j_is_SplitDipole)
530	<	d_j = data2.split_dipole_distance;
789	>	if (a_is_Fluctuating) {
790	>	C_a += *(idat.flucQ1);
791	>	}
792
793	<	duduz_j = V3Zero;
793	>	if (idat.excluded) {
794	>	*(idat.skippedCharge2) += C_a;
795	>	}
796	>	Eb -= C_a *  pre11_ * v02 * rhat;
797		}
798
799	<	if (j_is_Quadrupole) {
800	<	Q_j = data2.quadrupole_moments;
801	<	qxx_j = Q_j.x();
802	<	qyy_j = Q_j.y();
803	<	qzz_j = Q_j.z();
540	<
541	<	ux_j = idat.eFrame2.getColumn(0);
542	<	uy_j = idat.eFrame2.getColumn(1);
543	<	uz_j = idat.eFrame2.getColumn(2);
544	<
545	<	cx_j = dot(ux_j, rhat);
546	<	cy_j = dot(uy_j, rhat);
547	<	cz_j = dot(uz_j, rhat);
548	<
549	<	dudux_j = V3Zero;
550	<	duduy_j = V3Zero;
551	<	duduz_j = V3Zero;
799	>	if (a_is_Dipole) {
800	>	D_a = *(idat.dipole1);
801	>	rdDa = dot(rhat, D_a);
802	>	rxDa = cross(rhat, D_a);
803	>	Eb -=  pre12_ * (v13 * rdDa * rhat + v12 * D_a);
804		}
805
806	<	epot = 0.0;
807	<	dVdr = V3Zero;
806	>	if (a_is_Quadrupole) {
807	>	Q_a = *(idat.quadrupole1);
808	>	trQa =  Q_a.trace();
809	>	Qar =   Q_a * rhat;
810	>	rQa = rhat * Q_a;
811	>	rdQar = dot(rhat, Qar);
812	>	rxQar = cross(rhat, Qar);
813	>	Eb -= pre14_ * ((trQa * rhat + 2.0 * Qar) * v23 + rdQar * rhat * v24);
814	>	}
815
816	<	if (i_is_Charge) {
816	>	if (b_is_Charge) {
817	>	C_b = data2.fixedCharge;
818
819	<	if (j_is_Charge) {
820	<	if (screeningMethod_ == DAMPED) {
821	<	// assemble the damping variables
822	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
823	<	erfcVal = res.first;
824	<	derfcVal = res.second;
825	<	c1 = erfcVal * riji;
826	<	c2 = (-derfcVal + c1) * riji;
827	<	} else {
828	<	c1 = riji;
829	<	c2 = c1 * riji;
830	<	}
819	>	if (b_is_Fluctuating)
820	>	C_b += *(idat.flucQ2);
821	>
822	>	if (idat.excluded) {
823	>	*(idat.skippedCharge1) += C_b;
824	>	}
825	>	Ea += C_b *  pre11_ * v02 * rhat;
826	>	}
827	>
828	>	if (b_is_Dipole) {
829	>	D_b = *(idat.dipole2);
830	>	rdDb = dot(rhat, D_b);
831	>	rxDb = cross(rhat, D_b);
832	>	Ea += pre12_ * (v13 * rdDb * rhat + v12 * D_b);
833	>	}
834	>
835	>	if (b_is_Quadrupole) {
836	>	Q_b = *(idat.quadrupole2);
837	>	trQb =  Q_b.trace();
838	>	Qbr =   Q_b * rhat;
839	>	rQb = rhat * Q_b;
840	>	rdQbr = dot(rhat, Qbr);
841	>	rxQbr = cross(rhat, Qbr);
842	>	Ea += pre14_ * ((trQb * rhat + 2.0 * Qbr) * v23 + rdQbr * rhat * v24);
843	>	}
844	>
845	>	if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) {
846	>	J = Jij[idat.atypes];
847	>	}
848	>
849	>	if (a_is_Charge) {
850	>
851	>	if (b_is_Charge) {
852	>	pref =  pre11_ * *(idat.electroMult);
853	>	U  += C_a * C_b * pref * v01;
854	>	F  += C_a * C_b * pref * v02 * rhat;
855	>
856	>	// If this is an excluded pair, there are still indirect
857	>	// interactions via the reaction field we must worry about:
858
859	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
859	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
860	>	rfContrib = preRF_ * pref * C_a * C_b * *(idat.r2);
861	>	indirect_Pot += rfContrib;
862	>	indirect_F   += rfContrib * 2.0 * ri * rhat;
863	>	}
864
865	<	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
866	<	vterm = preVal * (c1 - c1c_);
867	<	dudr  = -idat.sw * preVal * c2;
865	>	// Fluctuating charge forces are handled via Coulomb integrals
866	>	// for excluded pairs (i.e. those connected via bonds) and
867	>	// with the standard charge-charge interaction otherwise.
868
869	<	} else if (summationMethod_ == esm_SHIFTED_FORCE)  {
870	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - cutoffRadius_) );
871	<	dudr  = idat.sw * preVal * (c2c_ - c2);
869	>	if (idat.excluded) {
870	>	if (a_is_Fluctuating || b_is_Fluctuating) {
871	>	coulInt = J->getValueAt( *(idat.rij) );
872	>	if (a_is_Fluctuating)  dUdCa += coulInt * C_b;
873	>	if (b_is_Fluctuating)  dUdCb += coulInt * C_a;
874	>	excluded_Pot += C_a * C_b * coulInt;
875	>	}
876	>	} else {
877	>	if (a_is_Fluctuating) dUdCa += C_b * pref * v01;
878	>	if (a_is_Fluctuating) dUdCb += C_a * pref * v01;
879	>	}
880	>	}
881
882	<	} else if (summationMethod_ == esm_REACTION_FIELD) {
883	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
884	<	vterm = preVal * ( riji + rfVal );
885	<	dudr  = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
882	>	if (b_is_Dipole) {
883	>	pref =  pre12_ * *(idat.electroMult);
884	>	U  += C_a * pref * v11 * rdDb;
885	>	F  += C_a * pref * (v13 * rdDb * rhat + v12 * D_b);
886	>	Tb += C_a * pref * v11 * rxDb;
887
888	<	} else {
588	<	vterm = preVal * riji * erfcVal;
888	>	if (a_is_Fluctuating) dUdCa += pref * v11 * rdDb;
889
890	<	dudr  = - idat.sw * preVal * c2;
890	>	// Even if we excluded this pair from direct interactions, we
891	>	// still have the reaction-field-mediated charge-dipole
892	>	// interaction:
893
894	+	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
895	+	rfContrib = C_a * pref * preRF_ * 2.0 * *(idat.rij);
896	+	indirect_Pot += rfContrib * rdDb;
897	+	indirect_F   += rfContrib * D_b / (*idat.rij);
898	+	indirect_Tb  += C_a * pref * preRF_ * rxDb;
899		}
593	–
594	–	idat.vpair += vterm;
595	–	epot += idat.sw * vterm;
596	–
597	–	dVdr += dudr * rhat;
900		}
901
902	<	if (j_is_Dipole) {
903	<	// pref is used by all the possible methods
904	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
905	<	preSw = idat.sw * pref;
902	>	if (b_is_Quadrupole) {
903	>	pref = pre14_ * *(idat.electroMult);
904	>	U  +=  C_a * pref * (v21 * trQb + v22 * rdQbr);
905	>	F  +=  C_a * pref * (trQb * rhat + 2.0 * Qbr) * v23;
906	>	F  +=  C_a * pref * rdQbr * rhat * v24;
907	>	Tb +=  C_a * pref * 2.0 * rxQbr * v22;
908
909	<	if (summationMethod_ == esm_REACTION_FIELD) {
910	<	ri2 = riji * riji;
911	<	ri3 = ri2 * riji;
608	<
609	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
610	<	idat.vpair += vterm;
611	<	epot += idat.sw * vterm;
909	>	if (a_is_Fluctuating) dUdCa += pref * (v21 * trQb + v22 * rdQbr);
910	>	}
911	>	}
912
913	<	dVdr +=  -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
614	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
913	>	if (a_is_Dipole) {
914
915	<	} else {
916	<	// determine the inverse r used if we have split dipoles
618	<	if (j_is_SplitDipole) {
619	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
620	<	ri = 1.0 / BigR;
621	<	scale = idat.rij * ri;
622	<	} else {
623	<	ri = riji;
624	<	scale = 1.0;
625	<	}
626	<
627	<	sc2 = scale * scale;
915	>	if (b_is_Charge) {
916	>	pref = pre12_ * *(idat.electroMult);
917
918	<	if (screeningMethod_ == DAMPED) {
919	<	// assemble the damping variables
920	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
632	<	erfcVal = res.first;
633	<	derfcVal = res.second;
634	<	c1 = erfcVal * ri;
635	<	c2 = (-derfcVal + c1) * ri;
636	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
637	<	} else {
638	<	c1 = ri;
639	<	c2 = c1 * ri;
640	<	c3 = 3.0 * c2 * ri;
641	<	}
642	<
643	<	c2ri = c2 * ri;
918	>	U  -= C_b * pref * v11 * rdDa;
919	>	F  -= C_b * pref * (v13 * rdDa * rhat + v12 * D_a);
920	>	Ta -= C_b * pref * v11 * rxDa;
921
922	<	// calculate the potential
646	<	pot_term =  scale * c2;
647	<	vterm = -pref * ct_j * pot_term;
648	<	idat.vpair += vterm;
649	<	epot += idat.sw * vterm;
650	<
651	<	// calculate derivatives for forces and torques
922	>	if (b_is_Fluctuating) dUdCb -= pref * v11 * rdDa;
923
924	<	dVdr += -preSw * (uz_j * c2ri - ct_j * rhat * sc2 * c3);
925	<	duduz_j += -preSw * pot_term * rhat;
926	<
924	>	// Even if we excluded this pair from direct interactions,
925	>	// we still have the reaction-field-mediated charge-dipole
926	>	// interaction:
927	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
928	>	rfContrib = C_b * pref * preRF_ * 2.0 * *(idat.rij);
929	>	indirect_Pot -= rfContrib * rdDa;
930	>	indirect_F   -= rfContrib * D_a / (*idat.rij);
931	>	indirect_Ta  -= C_b * pref * preRF_ * rxDa;
932		}
933		}
934
935	<	if (j_is_Quadrupole) {
936	<	// first precalculate some necessary variables
937	<	cx2 = cx_j * cx_j;
938	<	cy2 = cy_j * cy_j;
939	<	cz2 = cz_j * cz_j;
940	<	pref =  idat.electroMult * pre14_ * q_i * one_third_;
941	<
942	<	if (screeningMethod_ == DAMPED) {
943	<	// assemble the damping variables
944	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
945	<	erfcVal = res.first;
946	<	derfcVal = res.second;
947	<	c1 = erfcVal * riji;
948	<	c2 = (-derfcVal + c1) * riji;
949	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
950	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
951	<	} else {
952	<	c1 = riji;
953	<	c2 = c1 * riji;
678	<	c3 = 3.0 * c2 * riji;
679	<	c4 = 5.0 * c3 * riji * riji;
935	>	if (b_is_Dipole) {
936	>	pref = pre22_ * *(idat.electroMult);
937	>	DadDb = dot(D_a, D_b);
938	>	DaxDb = cross(D_a, D_b);
939	>
940	>	U  -= pref * (DadDb * v21 + rdDa * rdDb * v22);
941	>	F  -= pref * (DadDb * rhat + rdDb * D_a + rdDa * D_b)*v23;
942	>	F  -= pref * (rdDa * rdDb) * v24 * rhat;
943	>	Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa);
944	>	Tb += pref * (-v21 * DaxDb + v22 * rdDa * rxDb);
945	>
946	>	// Even if we excluded this pair from direct interactions, we
947	>	// still have the reaction-field-mediated dipole-dipole
948	>	// interaction:
949	>	if (summationMethod_ == esm_REACTION_FIELD && idat.excluded) {
950	>	rfContrib = -pref * preRF_ * 2.0;
951	>	indirect_Pot += rfContrib * DadDb;
952	>	indirect_Ta  += rfContrib * DaxDb;
953	>	indirect_Tb  -= rfContrib * DaxDb;
954		}
955
956	<	// precompute variables for convenience
683	<	preSw = idat.sw * pref;
684	<	c2ri = c2 * riji;
685	<	c3ri = c3 * riji;
686	<	c4rij = c4 * idat.rij;
687	<	rhatdot2 = 2.0 * rhat * c3;
688	<	rhatc4 = rhat * c4rij;
956	>	}
957
958	<	// calculate the potential
959	<	pot_term = ( qxx_j * (cx2*c3 - c2ri) +
960	<	qyy_j * (cy2*c3 - c2ri) +
961	<	qzz_j * (cz2*c3 - c2ri) );
962	<	vterm = pref * pot_term;
695	<	idat.vpair += vterm;
696	<	epot += idat.sw * vterm;
697	<
698	<	// calculate derivatives for the forces and torques
958	>	if (b_is_Quadrupole) {
959	>	pref = pre24_ * *(idat.electroMult);
960	>	DadQb = D_a * Q_b;
961	>	DadQbr = dot(D_a, Qbr);
962	>	DaxQbr = cross(D_a, Qbr);
963
964	<	dVdr += -preSw * ( qxx_j* (cx2*rhatc4 - (2.0*cx_j*ux_j + rhat)*c3ri) +
965	<	qyy_j* (cy2*rhatc4 - (2.0*cy_j*uy_j + rhat)*c3ri) +
966	<	qzz_j* (cz2*rhatc4 - (2.0*cz_j*uz_j + rhat)*c3ri));
967	<
968	<	dudux_j += preSw * qxx_j * cx_j * rhatdot2;
969	<	duduy_j += preSw * qyy_j * cy_j * rhatdot2;
970	<	duduz_j += preSw * qzz_j * cz_j * rhatdot2;
964	>	U  -= pref * ((trQb*rdDa + 2.0*DadQbr)*v31 + rdDa*rdQbr*v32);
965	>	F  -= pref * (trQb*D_a + 2.0*DadQb) * v33;
966	>	F  -= pref * (trQb*rdDa*rhat + 2.0*DadQbr*rhat + D_a*rdQbr
967	>	+ 2.0*rdDa*rQb)*v34;
968	>	F  -= pref * (rdDa * rdQbr * rhat * v35);
969	>	Ta += pref * ((-trQb*rxDa + 2.0 * DaxQbr)*v31 - rxDa*rdQbr*v32);
970	>	Tb += pref * ((2.0*cross(DadQb, rhat) - 2.0*DaxQbr)*v31
971	>	- 2.0*rdDa*rxQbr*v32);
972		}
973		}
709	–
710	–	if (i_is_Dipole) {
974
975	<	if (j_is_Charge) {
976	<	// variables used by all the methods
977	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
978	<	preSw = idat.sw * pref;
975	>	if (a_is_Quadrupole) {
976	>	if (b_is_Charge) {
977	>	pref = pre14_ * *(idat.electroMult);
978	>	U  += C_b * pref * (v21 * trQa + v22 * rdQar);
979	>	F  += C_b * pref * (trQa * rhat + 2.0 * Qar) * v23;
980	>	F  += C_b * pref * rdQar * rhat * v24;
981	>	Ta += C_b * pref * 2.0 * rxQar * v22;
982
983	<	if (summationMethod_ == esm_REACTION_FIELD) {
983	>	if (b_is_Fluctuating) dUdCb += pref * (v21 * trQa + v22 * rdQar);
984	>	}
985	>	if (b_is_Dipole) {
986	>	pref = pre24_ * *(idat.electroMult);
987	>	DbdQa = D_b * Q_a;
988	>	DbdQar = dot(D_b, Qar);
989	>	DbxQar = cross(D_b, Qar);
990
991	<	ri2 = riji * riji;
992	<	ri3 = ri2 * riji;
993	<
994	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
995	<	idat.vpair += vterm;
996	<	epot += idat.sw * vterm;
997	<
998	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
727	<
728	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
729	<
730	<	} else {
731	<
732	<	// determine inverse r if we are using split dipoles
733	<	if (i_is_SplitDipole) {
734	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
735	<	ri = 1.0 / BigR;
736	<	scale = idat.rij * ri;
737	<	} else {
738	<	ri = riji;
739	<	scale = 1.0;
740	<	}
741	<
742	<	sc2 = scale * scale;
743	<
744	<	if (screeningMethod_ == DAMPED) {
745	<	// assemble the damping variables
746	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
747	<	erfcVal = res.first;
748	<	derfcVal = res.second;
749	<	c1 = erfcVal * ri;
750	<	c2 = (-derfcVal + c1) * ri;
751	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
752	<	} else {
753	<	c1 = ri;
754	<	c2 = c1 * ri;
755	<	c3 = 3.0 * c2 * ri;
756	<	}
757	<
758	<	c2ri = c2 * ri;
759	<
760	<	// calculate the potential
761	<	pot_term = c2 * scale;
762	<	vterm = pref * ct_i * pot_term;
763	<	idat.vpair += vterm;
764	<	epot += idat.sw * vterm;
765	<
766	<	// calculate derivatives for the forces and torques
767	<	dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
768	<	duduz_i += preSw * pot_term * rhat;
769	<	}
991	>	U  += pref * ((trQa*rdDb + 2.0*DbdQar)*v31 + rdDb*rdQar*v32);
992	>	F  += pref * (trQa*D_b + 2.0*DbdQa) * v33;
993	>	F  += pref * (trQa*rdDb*rhat + 2.0*DbdQar*rhat + D_b*rdQar
994	>	+ 2.0*rdDb*rQa)*v34;
995	>	F  += pref * (rdDb * rdQar * rhat * v35);
996	>	Ta += pref * ((-2.0*cross(DbdQa, rhat) + 2.0*DbxQar)*v31
997	>	+ 2.0*rdDb*rxQar*v32);
998	>	Tb += pref * ((trQa*rxDb + 2.0 * DbxQar)*v31 + rxDb*rdQar*v32);
999		}
1000	+	if (b_is_Quadrupole) {
1001	+	pref = pre44_ * *(idat.electroMult);
1002	+	QaQb = Q_a * Q_b;
1003	+	trQaQb = QaQb.trace();
1004	+	rQaQb = rhat * QaQb;
1005	+	QaQbr = QaQb * rhat;
1006	+	QaxQb = cross(Q_a, Q_b);
1007
1008	<	if (j_is_Dipole) {
1009	<	// variables used by all methods
1010	<	ct_ij = dot(uz_i, uz_j);
1008	>	U  += pref * (trQa * trQb + 2.0*trQaQb) * v41;
1009	>	U  += pref * (trQa*rdQbr + trQb*rdQar  + 4.0*dot(rQa, Qbr)) * v42;
1010	>	U  += pref * (rdQar * rdQbr) * v43;
1011
1012	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
1013	<	preSw = idat.sw * pref;
1014	<
1015	<	if (summationMethod_ == esm_REACTION_FIELD) {
1016	<	ri2 = riji * riji;
1017	<	ri3 = ri2 * riji;
1018	<	ri4 = ri2 * ri2;
1012	>	F  += pref * (trQa*trQb*rhat + 2.0*trQaQb*rhat)*v44;
1013	>	F  += pref * (2.0*trQb*rQa + 2.0*trQa*rQb)*v44;
1014	>	F  += pref * (4.0* QaQb * rhat + 4.0 * rhat * QaQb)*v44;
1015	>	F  += pref * (trQa*rdQbr*rhat + trQb*rdQar*rhat
1016	>	+ 4.0*dot(rQa, Qbr)*rhat)*v45;
1017	>	F  += pref * (2.0*rQa*rdQbr + 2.0*rdQar*rQb)*v45;
1018	>	F  += pref * (rdQar*rdQbr*rhat) * v46;
1019
1020	<	vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
1021	<	preRF2_ * ct_ij );
1022	<	idat.vpair += vterm;
1023	<	epot += idat.sw * vterm;
1024	<
789	<	a1 = 5.0 * ct_i * ct_j - ct_ij;
790	<
791	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
1020	>	Ta += pref * (-4.0 * QaxQb  * v41);
1021	>	Ta += pref * (-2.0*trQb*cross(rQa, rhat)
1022	>	+ 4.0*cross(rhat, QaQbr)
1023	>	- 4.0*cross(rQa, Qbr)) * v42;
1024	>	Ta += pref * 2.0 * cross(rhat,Qar) * rdQbr * v43;
1025
1026	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
1027	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
1026	>	Tb += pref * (4.0 * QaxQb * v41);
1027	>	Tb += pref * (-2.0*trQa*cross(rQb, rhat)
1028	>	- 4.0*cross(rQaQb, rhat)
1029	>	+ 4.0*cross(rQa, Qbr))*v42;
1030	>	Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43;
1031
796	–	} else {
797	–
798	–	if (i_is_SplitDipole) {
799	–	if (j_is_SplitDipole) {
800	–	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
801	–	} else {
802	–	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
803	–	}
804	–	ri = 1.0 / BigR;
805	–	scale = idat.rij * ri;
806	–	} else {
807	–	if (j_is_SplitDipole) {
808	–	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
809	–	ri = 1.0 / BigR;
810	–	scale = idat.rij * ri;
811	–	} else {
812	–	ri = riji;
813	–	scale = 1.0;
814	–	}
815	–	}
816	–	if (screeningMethod_ == DAMPED) {
817	–	// assemble damping variables
818	–	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
819	–	erfcVal = res.first;
820	–	derfcVal = res.second;
821	–	c1 = erfcVal * ri;
822	–	c2 = (-derfcVal + c1) * ri;
823	–	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
824	–	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * ri * ri;
825	–	} else {
826	–	c1 = ri;
827	–	c2 = c1 * ri;
828	–	c3 = 3.0 * c2 * ri;
829	–	c4 = 5.0 * c3 * ri * ri;
830	–	}
831	–
832	–	// precompute variables for convenience
833	–	sc2 = scale * scale;
834	–	cti3 = ct_i * sc2 * c3;
835	–	ctj3 = ct_j * sc2 * c3;
836	–	ctidotj = ct_i * ct_j * sc2;
837	–	preSwSc = preSw * scale;
838	–	c2ri = c2 * ri;
839	–	c3ri = c3 * ri;
840	–	c4rij = c4 * idat.rij;
841	–
842	–	// calculate the potential
843	–	pot_term = (ct_ij * c2ri - ctidotj * c3);
844	–	vterm = pref * pot_term;
845	–	idat.vpair += vterm;
846	–	epot += idat.sw * vterm;
847	–
848	–	// calculate derivatives for the forces and torques
849	–	dVdr += preSwSc * ( ctidotj * rhat * c4rij  -
850	–	(ct_i*uz_j + ct_j*uz_i + ct_ij*rhat) * c3ri);
851	–
852	–	duduz_i += preSw * (uz_j * c2ri - ctj3 * rhat);
853	–	duduz_j += preSw * (uz_i * c2ri - cti3 * rhat);
854	–	}
1032		}
1033		}
1034
1035	<	if (i_is_Quadrupole) {
1036	<	if (j_is_Charge) {
1037	<	// precompute some necessary variables
1038	<	cx2 = cx_i * cx_i;
862	<	cy2 = cy_i * cy_i;
863	<	cz2 = cz_i * cz_i;
1035	>	if (idat.doElectricField) {
1036	>	*(idat.eField1) += Ea * *(idat.electroMult);
1037	>	*(idat.eField2) += Eb * *(idat.electroMult);
1038	>	}
1039
1040	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
1040	>	if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1041	>	if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1042
1043	<	if (screeningMethod_ == DAMPED) {
1044	<	// assemble the damping variables
1045	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
1046	<	erfcVal = res.first;
1047	<	derfcVal = res.second;
1048	<	c1 = erfcVal * riji;
1049	<	c2 = (-derfcVal + c1) * riji;
1050	<	c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
875	<	c4 = -4.0 * derfcVal * alpha4_ + 5.0 * c3 * riji * riji;
876	<	} else {
877	<	c1 = riji;
878	<	c2 = c1 * riji;
879	<	c3 = 3.0 * c2 * riji;
880	<	c4 = 5.0 * c3 * riji * riji;
881	<	}
882	<
883	<	// precompute some variables for convenience
884	<	preSw = idat.sw * pref;
885	<	c2ri = c2 * riji;
886	<	c3ri = c3 * riji;
887	<	c4rij = c4 * idat.rij;
888	<	rhatdot2 = 2.0 * rhat * c3;
889	<	rhatc4 = rhat * c4rij;
1043	>	if (!idat.excluded) {
1044	>
1045	>	*(idat.vpair) += U;
1046	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += U * *(idat.sw);
1047	>	*(idat.f1) += F * *(idat.sw);
1048	>
1049	>	if (a_is_Dipole || a_is_Quadrupole)
1050	>	*(idat.t1) += Ta * *(idat.sw);
1051
1052	<	// calculate the potential
1053	<	pot_term = ( qxx_i * (cx2 * c3 - c2ri) +
1054	<	qyy_i * (cy2 * c3 - c2ri) +
1055	<	qzz_i * (cz2 * c3 - c2ri) );
895	<
896	<	vterm = pref * pot_term;
897	<	idat.vpair += vterm;
898	<	epot += idat.sw * vterm;
1052	>	if (b_is_Dipole || b_is_Quadrupole)
1053	>	*(idat.t2) += Tb * *(idat.sw);
1054	>
1055	>	} else {
1056
1057	<	// calculate the derivatives for the forces and torques
1057	>	// only accumulate the forces and torques resulting from the
1058	>	// indirect reaction field terms.
1059
1060	<	dVdr += -preSw * (qxx_i* (cx2*rhatc4 - (2.0*cx_i*ux_i + rhat)*c3ri) +
1061	<	qyy_i* (cy2*rhatc4 - (2.0*cy_i*uy_i + rhat)*c3ri) +
1062	<	qzz_i* (cz2*rhatc4 - (2.0*cz_i*uz_i + rhat)*c3ri));
1063	<
1064	<	dudux_i += preSw * qxx_i * cx_i *  rhatdot2;
1065	<	duduy_i += preSw * qyy_i * cy_i *  rhatdot2;
1066	<	duduz_i += preSw * qzz_i * cz_i *  rhatdot2;
1067	<	}
1060	>	*(idat.vpair) += indirect_Pot;
1061	>	(*(idat.excludedPot))[ELECTROSTATIC_FAMILY] +=  excluded_Pot;
1062	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += *(idat.sw) * indirect_Pot;
1063	>	*(idat.f1) += *(idat.sw) * indirect_F;
1064	>
1065	>	if (a_is_Dipole || a_is_Quadrupole)
1066	>	*(idat.t1) += *(idat.sw) * indirect_Ta;
1067	>
1068	>	if (b_is_Dipole || b_is_Quadrupole)
1069	>	*(idat.t2) += *(idat.sw) * indirect_Tb;
1070		}
911	–
912	–	idat.pot += epot;
913	–	idat.f1 += dVdr;
914	–
915	–	if (i_is_Dipole || i_is_Quadrupole)
916	–	idat.t1 -= cross(uz_i, duduz_i);
917	–	if (i_is_Quadrupole) {
918	–	idat.t1 -= cross(ux_i, dudux_i);
919	–	idat.t1 -= cross(uy_i, duduy_i);
920	–	}
921	–
922	–	if (j_is_Dipole || j_is_Quadrupole)
923	–	idat.t2 -= cross(uz_j, duduz_j);
924	–	if (j_is_Quadrupole) {
925	–	idat.t2 -= cross(uz_j, dudux_j);
926	–	idat.t2 -= cross(uz_j, duduy_j);
927	–	}
928	–
1071		return;
1072		}
1073	+
1074	+	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1075
932	–	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
933	–
1076		if (!initialized_) initialize();
1077	+
1078	+	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1079
936	–	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
937	–	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
938	–
1080		// logicals
1081	<
1082	<	bool i_is_Charge = data1.is_Charge;
1083	<	bool i_is_Dipole = data1.is_Dipole;
1084	<
1085	<	bool j_is_Charge = data2.is_Charge;
945	<	bool j_is_Dipole = data2.is_Dipole;
946	<
947	<	RealType q_i, q_j;
1081	>	bool i_is_Charge = data.is_Charge;
1082	>	bool i_is_Dipole = data.is_Dipole;
1083	>	bool i_is_Fluctuating = data.is_Fluctuating;
1084	>	RealType C_a = data.fixedCharge;
1085	>	RealType self, preVal, DadDa;
1086
1087	<	// The skippedCharge computation is needed by the real-space cutoff methods
1088	<	// (i.e. shifted force and shifted potential)
1089	<
1090	<	if (i_is_Charge) {
1091	<	q_i = data1.charge;
1092	<	skdat.skippedCharge2 += q_i;
1087	>	if (i_is_Fluctuating) {
1088	>	C_a += *(sdat.flucQ);
1089	>	// dVdFQ is really a force, so this is negative the derivative
1090	>	*(sdat.dVdFQ) -=  *(sdat.flucQ) * data.hardness + data.electronegativity;
1091	>	(*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) *
1092	>	(*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity);
1093		}
1094
1095	<	if (j_is_Charge) {
1096	<	q_j = data2.charge;
959	<	skdat.skippedCharge1 += q_j;
960	<	}
961	<
962	<	// the rest of this function should only be necessary for reaction field.
963	<
964	<	if (summationMethod_ == esm_REACTION_FIELD) {
965	<	RealType riji, ri2, ri3;
966	<	RealType q_i, mu_i, ct_i;
967	<	RealType q_j, mu_j, ct_j;
968	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
969	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
970	<
971	<	// some variables we'll need independent of electrostatic type:
1095	>	switch (summationMethod_) {
1096	>	case esm_REACTION_FIELD:
1097
973	–	riji = 1.0 / skdat.rij;
974	–	rhat = skdat.d  * riji;
975	–
976	–	if (i_is_Dipole) {
977	–	mu_i = data1.dipole_moment;
978	–	uz_i = skdat.eFrame1.getColumn(2);
979	–	ct_i = dot(uz_i, rhat);
980	–	duduz_i = V3Zero;
981	–	}
982	–
983	–	if (j_is_Dipole) {
984	–	mu_j = data2.dipole_moment;
985	–	uz_j = skdat.eFrame2.getColumn(2);
986	–	ct_j = dot(uz_j, rhat);
987	–	duduz_j = V3Zero;
988	–	}
989	–
1098		if (i_is_Charge) {
1099	<	if (j_is_Charge) {
1100	<	preVal = skdat.electroMult * pre11_ * q_i * q_j;
1101	<	rfVal = preRF_ * skdat.rij * skdat.rij;
1102	<	vterm = preVal * rfVal;
1103	<	myPot += skdat.sw * vterm;
996	<	dudr  = skdat.sw * preVal * 2.0 * rfVal * riji;
997	<	dVdr += dudr * rhat;
998	<	}
999	<
1000	<	if (j_is_Dipole) {
1001	<	ri2 = riji * riji;
1002	<	ri3 = ri2 * riji;
1003	<	pref = skdat.electroMult * pre12_ * q_i * mu_j;
1004	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
1005	<	myPot += skdat.sw * vterm;
1006	<	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
1007	<	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1008	<	}
1099	>	// Self potential [see Wang and Hermans, "Reaction Field
1100	>	// Molecular Dynamics Simulation with Friedman’s Image Charge
1101	>	// Method," J. Phys. Chem. 99, 12001-12007 (1995).]
1102	>	preVal = pre11_ * preRF_ * C_a * C_a;
1103	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 * preVal / cutoffRadius_;
1104		}
1105	+
1106		if (i_is_Dipole) {
1107	<	if (j_is_Charge) {
1108	<	ri2 = riji * riji;
1013	<	ri3 = ri2 * riji;
1014	<	pref = skdat.electroMult * pre12_ * q_j * mu_i;
1015	<	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
1016	<	myPot += skdat.sw * vterm;
1017	<	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
1018	<	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
1019	<	}
1107	>	DadDa = data.dipole.lengthSquare();
1108	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DadDa;
1109		}
1110
1111	<	// accumulate the forces and torques resulting from the self term
1023	<	skdat.pot += myPot;
1024	<	skdat.f1 += dVdr;
1111	>	break;
1112
1113	<	if (i_is_Dipole)
1114	<	skdat.t1 -= cross(uz_i, duduz_i);
1028	<	if (j_is_Dipole)
1029	<	skdat.t2 -= cross(uz_j, duduz_j);
1030	<	}
1031	<	}
1032	<
1033	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1034	<	RealType mu1, preVal, chg1, self;
1035	<
1036	<	if (!initialized_) initialize();
1037	<
1038	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1039	<
1040	<	// logicals
1041	<
1042	<	bool i_is_Charge = data.is_Charge;
1043	<	bool i_is_Dipole = data.is_Dipole;
1044	<
1045	<	if (summationMethod_ == esm_REACTION_FIELD) {
1046	<	if (i_is_Dipole) {
1047	<	mu1 = data.dipole_moment;
1048	<	preVal = pre22_ * preRF2_ * mu1 * mu1;
1049	<	scdat.pot -= 0.5 * preVal;
1050	<
1051	<	// The self-correction term adds into the reaction field vector
1052	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1053	<	Vector3d ei = preVal * uz_i;
1054	<
1055	<	// This looks very wrong.  A vector crossed with itself is zero.
1056	<	scdat.t -= cross(uz_i, ei);
1057	<	}
1058	<	} else if (summationMethod_ == esm_SHIFTED_FORCE || summationMethod_ == esm_SHIFTED_POTENTIAL) {
1113	>	case esm_SHIFTED_FORCE:
1114	>	case esm_SHIFTED_POTENTIAL:
1115		if (i_is_Charge) {
1116	<	chg1 = data.charge;
1117	<	if (screeningMethod_ == DAMPED) {
1062	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1063	<	} else {
1064	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1065	<	}
1066	<	scdat.pot += self;
1116	>	self = -0.5 * selfMult_ * C_a * (C_a + *(sdat.skippedCharge)) * pre11_;
1117	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1118		}
1119	+	break;
1120	+	default:
1121	+	break;
1122		}
1123		}
1124	<
1125	<	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1124	>
1125	>	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
1126		// This seems to work moderately well as a default.  There's no
1127		// inherent scale for 1/r interactions that we can standardize.
1128		// 12 angstroms seems to be a reasonably good guess for most

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