[ViewVC] Diff of: OpenMD/branches/development/src/nonbonded/Electrostatic.cpp

Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1718 by gezelter, Thu May 24 01:29:59 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/MultipoleAdapter.hpp"
52	>	#include "io/Globals.hpp"
53	>	#include "nonbonded/SlaterIntegrals.hpp"
54	>	#include "utils/PhysicalConstants.hpp"
55
56
57		namespace OpenMD {
58
59		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
60	<	forceField_(NULL) {}
60	>	forceField_(NULL), info_(NULL),
61	>	haveCutoffRadius_(false),
62	>	haveDampingAlpha_(false),
63	>	haveDielectric_(false),
64	>	haveElectroSpline_(false)
65	>	{}
66
67		void Electrostatic::initialize() {
68	+
69	+	Globals* simParams_ = info_->getSimParams();
70	+
71	+	summationMap_["HARD"] = esm_HARD;
72	+	summationMap_["NONE"] = esm_HARD;
73	+	summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
74	+	summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL;
75	+	summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE;
76	+	summationMap_["REACTION_FIELD"] = esm_REACTION_FIELD;
77	+	summationMap_["EWALD_FULL"] = esm_EWALD_FULL;
78	+	summationMap_["EWALD_PME"] = esm_EWALD_PME;
79	+	summationMap_["EWALD_SPME"] = esm_EWALD_SPME;
80	+	screeningMap_["DAMPED"] = DAMPED;
81	+	screeningMap_["UNDAMPED"] = UNDAMPED;
82	+
83		// these prefactors convert the multipole interactions into kcal / mol
84		// all were computed assuming distances are measured in angstroms
85		// Charge-Charge, assuming charges are measured in electrons
#	Line 79 \| Line 104 \| namespace OpenMD {
104
105		// variables to handle different summation methods for long-range
106		// electrostatics:
107	<	summationMethod_ = NONE;
107	>	summationMethod_ = esm_HARD;
108		screeningMethod_ = UNDAMPED;
109		dielectric_ = 1.0;
110		one_third_ = 1.0 / 3.0;
86	–	haveDefaultCutoff_ = false;
87	–	haveDampingAlpha_ = false;
88	–	haveDielectric_ = false;
89	–	haveElectroSpline_ = false;
111
112	+	// check the summation method:
113	+	if (simParams_->haveElectrostaticSummationMethod()) {
114	+	string myMethod = simParams_->getElectrostaticSummationMethod();
115	+	toUpper(myMethod);
116	+	map<string, ElectrostaticSummationMethod>::iterator i;
117	+	i = summationMap_.find(myMethod);
118	+	if ( i != summationMap_.end() ) {
119	+	summationMethod_ = (*i).second;
120	+	} else {
121	+	// throw error
122	+	sprintf( painCave.errMsg,
123	+	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
124	+	"\t(Input file specified %s .)\n"
125	+	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
126	+	"\t\"shifted_potential\", \"shifted_force\", or \n"
127	+	"\t\"reaction_field\".\n", myMethod.c_str() );
128	+	painCave.isFatal = 1;
129	+	simError();
130	+	}
131	+	} else {
132	+	// set ElectrostaticSummationMethod to the cutoffMethod:
133	+	if (simParams_->haveCutoffMethod()){
134	+	string myMethod = simParams_->getCutoffMethod();
135	+	toUpper(myMethod);
136	+	map<string, ElectrostaticSummationMethod>::iterator i;
137	+	i = summationMap_.find(myMethod);
138	+	if ( i != summationMap_.end() ) {
139	+	summationMethod_ = (*i).second;
140	+	}
141	+	}
142	+	}
143	+
144	+	if (summationMethod_ == esm_REACTION_FIELD) {
145	+	if (!simParams_->haveDielectric()) {
146	+	// throw warning
147	+	sprintf( painCave.errMsg,
148	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
149	+	"\tA default value of %f will be used for the dielectric.\n", dielectric_);
150	+	painCave.isFatal = 0;
151	+	painCave.severity = OPENMD_INFO;
152	+	simError();
153	+	} else {
154	+	dielectric_ = simParams_->getDielectric();
155	+	}
156	+	haveDielectric_ = true;
157	+	}
158	+
159	+	if (simParams_->haveElectrostaticScreeningMethod()) {
160	+	string myScreen = simParams_->getElectrostaticScreeningMethod();
161	+	toUpper(myScreen);
162	+	map<string, ElectrostaticScreeningMethod>::iterator i;
163	+	i = screeningMap_.find(myScreen);
164	+	if ( i != screeningMap_.end()) {
165	+	screeningMethod_ = (*i).second;
166	+	} else {
167	+	sprintf( painCave.errMsg,
168	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
169	+	"\t(Input file specified %s .)\n"
170	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
171	+	"or \"damped\".\n", myScreen.c_str() );
172	+	painCave.isFatal = 1;
173	+	simError();
174	+	}
175	+	}
176	+
177	+	// check to make sure a cutoff value has been set:
178	+	if (!haveCutoffRadius_) {
179	+	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
180	+	"Cutoff value!\n");
181	+	painCave.severity = OPENMD_ERROR;
182	+	painCave.isFatal = 1;
183	+	simError();
184	+	}
185	+
186	+	if (screeningMethod_ == DAMPED) {
187	+	if (!simParams_->haveDampingAlpha()) {
188	+	// first set a cutoff dependent alpha value
189	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
190	+	dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
191	+	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
192	+
193	+	// throw warning
194	+	sprintf( painCave.errMsg,
195	+	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
196	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
197	+	dampingAlpha_, cutoffRadius_);
198	+	painCave.severity = OPENMD_INFO;
199	+	painCave.isFatal = 0;
200	+	simError();
201	+	} else {
202	+	dampingAlpha_ = simParams_->getDampingAlpha();
203	+	}
204	+	haveDampingAlpha_ = true;
205	+	}
206	+
207		// find all of the Electrostatic atom Types:
208		ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
209		ForceField::AtomTypeContainer::MapTypeIterator i;
210		AtomType* at;
211	<
211	>
212		for (at = atomTypes->beginType(i); at != NULL;
213		at = atomTypes->nextType(i)) {
214
#	Line 100 \| Line 216 \| namespace OpenMD {
216		addType(at);
217		}
218
103	–	// check to make sure a cutoff value has been set:
104	–	if (!haveDefaultCutoff_) {
105	–	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
106	–	"Cutoff value!\n");
107	–	painCave.severity = OPENMD_ERROR;
108	–	painCave.isFatal = 1;
109	–	simError();
110	–	}
219
220	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
221	<	rcuti_ = 1.0 / defaultCutoff_;
220	>	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
221	>	rcuti_ = 1.0 / cutoffRadius_;
222		rcuti2_ = rcuti_ * rcuti_;
223		rcuti3_ = rcuti2_ * rcuti_;
224		rcuti4_ = rcuti2_ * rcuti2_;
225
226		if (screeningMethod_ == DAMPED) {
227	<	if (!haveDampingAlpha_) {
120	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no "
121	<	"DampingAlpha value!\n");
122	<	painCave.severity = OPENMD_ERROR;
123	<	painCave.isFatal = 1;
124	<	simError();
125	<	}
126	<
227	>
228		alpha2_ = dampingAlpha_ * dampingAlpha_;
229		alpha4_ = alpha2_ * alpha2_;
230		alpha6_ = alpha4_ * alpha2_;
231		alpha8_ = alpha4_ * alpha4_;
232
233	<	constEXP_ = exp(-alpha2_ * defaultCutoff2_);
233	>	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
234		invRootPi_ = 0.56418958354775628695;
235		alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
236
237	<	c1c_ = erfc(dampingAlpha_ * defaultCutoff_) * rcuti_;
237	>	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
238		c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
239		c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
240		c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
#	Line 148 \| Line 249 \| namespace OpenMD {
249		c6c_ = 9.0 * c5c_ * rcuti2_;
250		}
251
252	<	if (summationMethod_ == REACTION_FIELD) {
253	<	if (haveDielectric_) {
254	<	preRF_ = (dielectric_ - 1.0) /
255	<	((2.0 * dielectric_ + 1.0) * defaultCutoff2_ * defaultCutoff_);
155	<	preRF2_ = 2.0 * preRF_;
156	<	} else {
157	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no Dielectric"
158	<	" value!\n");
159	<	painCave.severity = OPENMD_ERROR;
160	<	painCave.isFatal = 1;
161	<	simError();
162	<	}
252	>	if (summationMethod_ == esm_REACTION_FIELD) {
253	>	preRF_ = (dielectric_ - 1.0) /
254	>	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
255	>	preRF2_ = 2.0 * preRF_;
256		}
257	<
258	<	RealType dx = defaultCutoff_ / RealType(np_ - 1);
257	>
258	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
259	>	// have charged atoms longer than the cutoffRadius away from each
260	>	// other. Splining may not be the best choice here. Direct calls
261	>	// to erfc might be preferrable.
262	>
263	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
264		RealType rval;
265		vector<RealType> rvals;
266		vector<RealType> yvals;
#	Line 186 \| Line 284 \| namespace OpenMD {
284		electrostaticAtomData.is_SplitDipole = false;
285		electrostaticAtomData.is_Quadrupole = false;
286
287	<	if (atomType->isCharge()) {
190	<	GenericData* data = atomType->getPropertyByName("Charge");
287	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
288
289	<	if (data == NULL) {
193	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
194	<	"Charge\n"
195	<	"\tparameters for atomType %s.\n",
196	<	atomType->getName().c_str());
197	<	painCave.severity = OPENMD_ERROR;
198	<	painCave.isFatal = 1;
199	<	simError();
200	<	}
201	<
202	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
203	<	if (doubleData == NULL) {
204	<	sprintf( painCave.errMsg,
205	<	"Electrostatic::addType could not convert GenericData to "
206	<	"Charge for\n"
207	<	"\tatom type %s\n", atomType->getName().c_str());
208	<	painCave.severity = OPENMD_ERROR;
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
289	>	if (fca.isFixedCharge()) {
290		electrostaticAtomData.is_Charge = true;
291	<	electrostaticAtomData.charge = doubleData->getData();
291	>	electrostaticAtomData.charge = fca.getCharge();
292		}
293
294	<	if (atomType->isDirectional()) {
295	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
296	<
219	<	if (daType->isDipole()) {
220	<	GenericData* data = daType->getPropertyByName("Dipole");
221	<
222	<	if (data == NULL) {
223	<	sprintf( painCave.errMsg,
224	<	"Electrostatic::addType could not find Dipole\n"
225	<	"\tparameters for atomType %s.\n",
226	<	daType->getName().c_str());
227	<	painCave.severity = OPENMD_ERROR;
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
231	<
232	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
233	<	if (doubleData == NULL) {
234	<	sprintf( painCave.errMsg,
235	<	"Electrostatic::addType could not convert GenericData to "
236	<	"Dipole Moment\n"
237	<	"\tfor atom type %s\n", daType->getName().c_str());
238	<	painCave.severity = OPENMD_ERROR;
239	<	painCave.isFatal = 1;
240	<	simError();
241	<	}
294	>	MultipoleAdapter ma = MultipoleAdapter(atomType);
295	>	if (ma.isMultipole()) {
296	>	if (ma.isDipole()) {
297		electrostaticAtomData.is_Dipole = true;
298	<	electrostaticAtomData.dipole_moment = doubleData->getData();
298	>	electrostaticAtomData.dipole_moment = ma.getDipoleMoment();
299		}
300	<
246	<	if (daType->isSplitDipole()) {
247	<	GenericData* data = daType->getPropertyByName("SplitDipoleDistance");
248	<
249	<	if (data == NULL) {
250	<	sprintf(painCave.errMsg,
251	<	"Electrostatic::addType could not find SplitDipoleDistance\n"
252	<	"\tparameter for atomType %s.\n",
253	<	daType->getName().c_str());
254	<	painCave.severity = OPENMD_ERROR;
255	<	painCave.isFatal = 1;
256	<	simError();
257	<	}
258	<
259	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
260	<	if (doubleData == NULL) {
261	<	sprintf( painCave.errMsg,
262	<	"Electrostatic::addType could not convert GenericData to "
263	<	"SplitDipoleDistance for\n"
264	<	"\tatom type %s\n", daType->getName().c_str());
265	<	painCave.severity = OPENMD_ERROR;
266	<	painCave.isFatal = 1;
267	<	simError();
268	<	}
300	>	if (ma.isSplitDipole()) {
301		electrostaticAtomData.is_SplitDipole = true;
302	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
302	>	electrostaticAtomData.split_dipole_distance = ma.getSplitDipoleDistance();
303		}
304	<
273	<	if (daType->isQuadrupole()) {
274	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
275	<
276	<	if (data == NULL) {
277	<	sprintf( painCave.errMsg,
278	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
279	<	"\tparameter for atomType %s.\n",
280	<	daType->getName().c_str());
281	<	painCave.severity = OPENMD_ERROR;
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
304	>	if (ma.isQuadrupole()) {
305		// Quadrupoles in OpenMD are set as the diagonal elements
306		// of the diagonalized traceless quadrupole moment tensor.
307		// The column vectors of the unitary matrix that diagonalizes
308		// the quadrupole moment tensor become the eFrame (or the
309		// electrostatic version of the body-fixed frame.
291	–
292	–	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
293	–	if (v3dData == NULL) {
294	–	sprintf( painCave.errMsg,
295	–	"Electrostatic::addType could not convert GenericData to "
296	–	"Quadrupole Moments for\n"
297	–	"\tatom type %s\n", daType->getName().c_str());
298	–	painCave.severity = OPENMD_ERROR;
299	–	painCave.isFatal = 1;
300	–	simError();
301	–	}
310		electrostaticAtomData.is_Quadrupole = true;
311	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
311	>	electrostaticAtomData.quadrupole_moments = ma.getQuadrupoleMoments();
312		}
313		}
314
315	<	AtomTypeProperties atp = atomType->getATP();
315	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
316
317	+	if (fqa.isFluctuatingCharge()) {
318	+	electrostaticAtomData.is_FluctuatingCharge = true;
319	+	electrostaticAtomData.electronegativity = fca.getElectronegativity();
320	+	electrostaticAtomData.hardness = fca.getHardness();
321	+	electrostaticAtomData.slaterN = fca.getSlaterN();
322	+	electrostaticAtomData.slaterZeta = fca.getSlaterZeta();
323	+	}
324	+
325		pair<map<int,AtomType*>::iterator,bool> ret;
326	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
326	>	ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
327	>	atomType) );
328		if (ret.second == false) {
329		sprintf( painCave.errMsg,
330		"Electrostatic already had a previous entry with ident %d\n",
331	<	atp.ident);
331	>	atomType->getIdent() );
332		painCave.severity = OPENMD_INFO;
333		painCave.isFatal = 0;
334		simError();
335		}
336
337	<	ElectrostaticMap[atomType] = electrostaticAtomData;
337	>	ElectrostaticMap[atomType] = electrostaticAtomData;
338	>
339	>	// Now, iterate over all known types and add to the mixing map:
340	>
341	>	map<AtomType*, ElectrostaticAtomData>::iterator it;
342	>	for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
343	>	AtomType* atype2 = (*it).first;
344	>
345	>	if ((*it).is_FluctuatingCharge && electrostaticAtomData.is_FluctuatingCharge) {
346	>
347	>	RealType a = electrostaticAtomData.slaterZeta;
348	>	RealType b = (*it).slaterZeta;
349	>	int m = electrostaticAtomData.slaterN;
350	>	int n = (*it).slaterN;
351	>
352	>	// Create the spline of the coulombic integral for s-type
353	>	// Slater orbitals. Add a 2 angstrom safety window to deal
354	>	// with cutoffGroups that have charged atoms longer than the
355	>	// cutoffRadius away from each other.
356	>
357	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
358	>	vector<RealType> rvals;
359	>	vector<RealType> J1vals;
360	>	vector<RealType> J2vals;
361	>	for (int i = 0; i < np_; i++) {
362	>	rval = RealType(i) * dr;
363	>	rvals.push_back(rval);
364	>	J1vals.push_back( sSTOCoulInt( a, b, m, n, rval * PhysicalConstants::angstromsToBohr ) );
365	>	J2vals.push_back( sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) );
366	>	}
367	>
368	>	CubicSpline J1 = new CubicSpline();
369	>	J1->addPoints(rvals, J1vals);
370	>	CubicSpline J2 = new CubicSpline();
371	>	J2->addPoints(rvals, J2vals);
372	>
373	>	pair<AtomType, AtomType> key1, key2;
374	>	key1 = make_pair(atomType, atype2);
375	>	key2 = make_pair(atype2, atomType);
376	>
377	>	Jij[key1] = J1;
378	>	Jij[key2] = J2;
379	>	}
380	>	}
381	>
382		return;
383		}
384
385	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
386	<	RealType theRSW ) {
387	<	defaultCutoff_ = theECR;
388	<	rrf_ = defaultCutoff_;
328	<	rt_ = theRSW;
329	<	haveDefaultCutoff_ = true;
385	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
386	>	cutoffRadius_ = rCut;
387	>	rrf_ = cutoffRadius_;
388	>	haveCutoffRadius_ = true;
389		}
390	+
391	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
392	+	rt_ = rSwitch;
393	+	}
394		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
395		summationMethod_ = esm;
396		}
#	Line 343 \| Line 406 \| namespace OpenMD {
406		haveDielectric_ = true;
407		}
408
409	<	void Electrostatic::calcForce(InteractionData idat) {
409	>	void Electrostatic::calcForce(InteractionData &idat) {
410
411		// utility variables. Should clean these up and use the Vector3d and
412		// Mat3x3d to replace as many as we can in future versions:
#	Line 357 \| Line 420 \| namespace OpenMD {
420		RealType ct_i, ct_j, ct_ij, a1;
421		RealType riji, ri, ri2, ri3, ri4;
422		RealType pref, vterm, epot, dudr;
423	+	RealType vpair(0.0);
424		RealType scale, sc2;
425		RealType pot_term, preVal, rfVal;
426		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
427		RealType preSw, preSwSc;
428		RealType c1, c2, c3, c4;
429	<	RealType erfcVal, derfcVal;
429	>	RealType erfcVal(1.0), derfcVal(0.0);
430		RealType BigR;
431	+	RealType two(2.0), three(3.0);
432
433		Vector3d Q_i, Q_j;
434		Vector3d ux_i, uy_i, uz_i;
#	Line 373 \| Line 438 \| namespace OpenMD {
438		Vector3d rhatdot2, rhatc4;
439		Vector3d dVdr;
440
441	+	// variables for indirect (reaction field) interactions for excluded pairs:
442	+	RealType indirect_Pot(0.0);
443	+	RealType indirect_vpair(0.0);
444	+	Vector3d indirect_dVdr(V3Zero);
445	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
446	+
447		pair<RealType, RealType> res;
448
449		if (!initialized_) initialize();
450
451	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
452	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
451	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
452	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
453
454		// some variables we'll need independent of electrostatic type:
455
456	<	riji = 1.0 / idat.rij;
457	<	Vector3d rhat = idat.d * riji;
456	>	riji = 1.0 / *(idat.rij) ;
457	>	Vector3d rhat = (idat.d) riji;
458
459		// logicals
460
#	Line 397 \| Line 468 \| namespace OpenMD {
468		bool j_is_SplitDipole = data2.is_SplitDipole;
469		bool j_is_Quadrupole = data2.is_Quadrupole;
470
471	<	if (i_is_Charge)
471	>	if (i_is_Charge) {
472		q_i = data1.charge;
473	+	if (idat.excluded) {
474	+	*(idat.skippedCharge2) += q_i;
475	+	}
476	+	}
477
478		if (i_is_Dipole) {
479		mu_i = data1.dipole_moment;
480	<	uz_i = idat.eFrame1.getColumn(2);
480	>	uz_i = idat.eFrame1->getColumn(2);
481
482		ct_i = dot(uz_i, rhat);
483
#	Line 418 \| Line 493 \| namespace OpenMD {
493		qyy_i = Q_i.y();
494		qzz_i = Q_i.z();
495
496	<	ux_i = idat.eFrame1.getColumn(0);
497	<	uy_i = idat.eFrame1.getColumn(1);
498	<	uz_i = idat.eFrame1.getColumn(2);
496	>	ux_i = idat.eFrame1->getColumn(0);
497	>	uy_i = idat.eFrame1->getColumn(1);
498	>	uz_i = idat.eFrame1->getColumn(2);
499
500		cx_i = dot(ux_i, rhat);
501		cy_i = dot(uy_i, rhat);
#	Line 431 \| Line 506 \| namespace OpenMD {
506		duduz_i = V3Zero;
507		}
508
509	<	if (j_is_Charge)
509	>	if (j_is_Charge) {
510		q_j = data2.charge;
511	+	if (idat.excluded) {
512	+	*(idat.skippedCharge1) += q_j;
513	+	}
514	+	}
515
516	+
517		if (j_is_Dipole) {
518		mu_j = data2.dipole_moment;
519	<	uz_j = idat.eFrame2.getColumn(2);
519	>	uz_j = idat.eFrame2->getColumn(2);
520
521		ct_j = dot(uz_j, rhat);
522
#	Line 452 \| Line 532 \| namespace OpenMD {
532		qyy_j = Q_j.y();
533		qzz_j = Q_j.z();
534
535	<	ux_j = idat.eFrame2.getColumn(0);
536	<	uy_j = idat.eFrame2.getColumn(1);
537	<	uz_j = idat.eFrame2.getColumn(2);
535	>	ux_j = idat.eFrame2->getColumn(0);
536	>	uy_j = idat.eFrame2->getColumn(1);
537	>	uz_j = idat.eFrame2->getColumn(2);
538
539		cx_j = dot(ux_j, rhat);
540		cy_j = dot(uy_j, rhat);
#	Line 473 \| Line 553 \| namespace OpenMD {
553		if (j_is_Charge) {
554		if (screeningMethod_ == DAMPED) {
555		// assemble the damping variables
556	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
557	<	erfcVal = res.first;
558	<	derfcVal = res.second;
556	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
557	>	//erfcVal = res.first;
558	>	//derfcVal = res.second;
559	>
560	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
561	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
562	>
563		c1 = erfcVal * riji;
564		c2 = (-derfcVal + c1) * riji;
565		} else {
#	Line 483 \| Line 567 \| namespace OpenMD {
567		c2 = c1 * riji;
568		}
569
570	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
570	>	preVal = (idat.electroMult) pre11_ * q_i * q_j;
571
572	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
572	>	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
573		vterm = preVal * (c1 - c1c_);
574	<	dudr = -idat.sw * preVal * c2;
574	>	dudr = - (idat.sw) preVal * c2;
575
576	<	} else if (summationMethod_ == SHIFTED_FORCE) {
577	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
578	<	dudr = idat.sw * preVal * (c2c_ - c2);
576	>	} else if (summationMethod_ == esm_SHIFTED_FORCE) {
577	>	vterm = preVal * ( c1 - c1c_ + c2c_( (idat.rij) - cutoffRadius_) );
578	>	dudr = (idat.sw) preVal * (c2c_ - c2);
579
580	<	} else if (summationMethod_ == REACTION_FIELD) {
581	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
580	>	} else if (summationMethod_ == esm_REACTION_FIELD) {
581	>	rfVal = preRF_ * (idat.rij) *(idat.rij);
582	>
583		vterm = preVal * ( riji + rfVal );
584	<	dudr = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
584	>	dudr = (idat.sw) preVal * ( 2.0 * rfVal - riji ) * riji;
585	>
586	>	// if this is an excluded pair, there are still indirect
587	>	// interactions via the reaction field we must worry about:
588
589	+	if (idat.excluded) {
590	+	indirect_vpair += preVal * rfVal;
591	+	indirect_Pot += (idat.sw) preVal * rfVal;
592	+	indirect_dVdr += (idat.sw) preVal * two * rfVal * riji * rhat;
593	+	}
594	+
595		} else {
502	–	vterm = preVal * riji * erfcVal;
596
597	<	dudr = - idat.sw * preVal * c2;
597	>	vterm = preVal * riji * erfcVal;
598	>	dudr = - (idat.sw) preVal * c2;
599
600		}
507	–
508	–	idat.vpair += vterm;
509	–	epot += idat.sw * vterm;
601
602	<	dVdr += dudr * rhat;
602	>	vpair += vterm;
603	>	epot += (idat.sw) vterm;
604	>	dVdr += dudr * rhat;
605		}
606
607		if (j_is_Dipole) {
608		// pref is used by all the possible methods
609	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
610	<	preSw = idat.sw * pref;
609	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
610	>	preSw = (idat.sw) pref;
611
612	<	if (summationMethod_ == REACTION_FIELD) {
612	>	if (summationMethod_ == esm_REACTION_FIELD) {
613		ri2 = riji * riji;
614		ri3 = ri2 * riji;
615
616	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
617	<	idat.vpair += vterm;
618	<	epot += idat.sw * vterm;
616	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
617	>	vpair += vterm;
618	>	epot += (idat.sw) vterm;
619
620	<	dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
621	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
620	>	dVdr += -preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
621	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
622
623	+	// Even if we excluded this pair from direct interactions,
624	+	// we still have the reaction-field-mediated charge-dipole
625	+	// interaction:
626	+
627	+	if (idat.excluded) {
628	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
629	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
630	+	indirect_dVdr += preSw * preRF2_ * uz_j;
631	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
632	+	}
633	+
634		} else {
635		// determine the inverse r used if we have split dipoles
636		if (j_is_SplitDipole) {
637	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
637	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
638		ri = 1.0 / BigR;
639	<	scale = idat.rij * ri;
639	>	scale = (idat.rij) ri;
640		} else {
641		ri = riji;
642		scale = 1.0;
#	Line 542 \| Line 646 \| namespace OpenMD {
646
647		if (screeningMethod_ == DAMPED) {
648		// assemble the damping variables
649	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
650	<	erfcVal = res.first;
651	<	derfcVal = res.second;
649	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
650	>	//erfcVal = res.first;
651	>	//derfcVal = res.second;
652	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
653	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
654		c1 = erfcVal * ri;
655		c2 = (-derfcVal + c1) * ri;
656		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 559 \| Line 665 \| namespace OpenMD {
665		// calculate the potential
666		pot_term = scale * c2;
667		vterm = -pref * ct_j * pot_term;
668	<	idat.vpair += vterm;
669	<	epot += idat.sw * vterm;
668	>	vpair += vterm;
669	>	epot += (idat.sw) vterm;
670
671		// calculate derivatives for forces and torques
672
#	Line 575 \| Line 681 \| namespace OpenMD {
681		cx2 = cx_j * cx_j;
682		cy2 = cy_j * cy_j;
683		cz2 = cz_j * cz_j;
684	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
684	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
685
686		if (screeningMethod_ == DAMPED) {
687		// assemble the damping variables
688	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
689	<	erfcVal = res.first;
690	<	derfcVal = res.second;
688	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
689	>	//erfcVal = res.first;
690	>	//derfcVal = res.second;
691	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
692	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
693		c1 = erfcVal * riji;
694		c2 = (-derfcVal + c1) * riji;
695		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 594 \| Line 702 \| namespace OpenMD {
702		}
703
704		// precompute variables for convenience
705	<	preSw = idat.sw * pref;
705	>	preSw = (idat.sw) pref;
706		c2ri = c2 * riji;
707		c3ri = c3 * riji;
708	<	c4rij = c4 * idat.rij;
709	<	rhatdot2 = 2.0 * rhat * c3;
708	>	c4rij = c4 * *(idat.rij) ;
709	>	rhatdot2 = two * rhat * c3;
710		rhatc4 = rhat * c4rij;
711
712		// calculate the potential
#	Line 606 \| Line 714 \| namespace OpenMD {
714		qyy_j * (cy2*c3 - c2ri) +
715		qzz_j * (cz2*c3 - c2ri) );
716		vterm = pref * pot_term;
717	<	idat.vpair += vterm;
718	<	epot += idat.sw * vterm;
717	>	vpair += vterm;
718	>	epot += (idat.sw) vterm;
719
720		// calculate derivatives for the forces and torques
721
722	<	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (2.0cx_jux_j + rhat)c3ri) +
723	<	qyy_j* (cy2rhatc4 - (2.0cy_juy_j + rhat)c3ri) +
724	<	qzz_j* (cz2rhatc4 - (2.0cz_juz_j + rhat)c3ri));
722	>	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (twocx_jux_j + rhat)c3ri) +
723	>	qyy_j* (cy2rhatc4 - (twocy_juy_j + rhat)c3ri) +
724	>	qzz_j* (cz2rhatc4 - (twocz_juz_j + rhat)c3ri));
725
726		dudux_j += preSw * qxx_j * cx_j * rhatdot2;
727		duduy_j += preSw * qyy_j * cy_j * rhatdot2;
#	Line 625 \| Line 733 \| namespace OpenMD {
733
734		if (j_is_Charge) {
735		// variables used by all the methods
736	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
737	<	preSw = idat.sw * pref;
736	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
737	>	preSw = (idat.sw) pref;
738
739	<	if (summationMethod_ == REACTION_FIELD) {
739	>	if (summationMethod_ == esm_REACTION_FIELD) {
740
741		ri2 = riji * riji;
742		ri3 = ri2 * riji;
743
744	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
745	<	idat.vpair += vterm;
746	<	epot += idat.sw * vterm;
744	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
745	>	vpair += vterm;
746	>	epot += (idat.sw) vterm;
747
748	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
748	>	dVdr += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_ * uz_i);
749
750	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
750	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
751	>
752	>	// Even if we excluded this pair from direct interactions,
753	>	// we still have the reaction-field-mediated charge-dipole
754	>	// interaction:
755	>
756	>	if (idat.excluded) {
757	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
758	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
759	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
760	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
761	>	}
762
763		} else {
764
765		// determine inverse r if we are using split dipoles
766		if (i_is_SplitDipole) {
767	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
767	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
768		ri = 1.0 / BigR;
769	<	scale = idat.rij * ri;
769	>	scale = (idat.rij) ri;
770		} else {
771		ri = riji;
772		scale = 1.0;
#	Line 657 \| Line 776 \| namespace OpenMD {
776
777		if (screeningMethod_ == DAMPED) {
778		// assemble the damping variables
779	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
780	<	erfcVal = res.first;
781	<	derfcVal = res.second;
779	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
780	>	//erfcVal = res.first;
781	>	//derfcVal = res.second;
782	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
783	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
784		c1 = erfcVal * ri;
785		c2 = (-derfcVal + c1) * ri;
786		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 674 \| Line 795 \| namespace OpenMD {
795		// calculate the potential
796		pot_term = c2 * scale;
797		vterm = pref * ct_i * pot_term;
798	<	idat.vpair += vterm;
799	<	epot += idat.sw * vterm;
798	>	vpair += vterm;
799	>	epot += (idat.sw) vterm;
800
801		// calculate derivatives for the forces and torques
802		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
#	Line 687 \| Line 808 \| namespace OpenMD {
808		// variables used by all methods
809		ct_ij = dot(uz_i, uz_j);
810
811	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
812	<	preSw = idat.sw * pref;
811	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
812	>	preSw = (idat.sw) pref;
813
814	<	if (summationMethod_ == REACTION_FIELD) {
814	>	if (summationMethod_ == esm_REACTION_FIELD) {
815		ri2 = riji * riji;
816		ri3 = ri2 * riji;
817		ri4 = ri2 * ri2;
818
819		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
820		preRF2_ * ct_ij );
821	<	idat.vpair += vterm;
822	<	epot += idat.sw * vterm;
821	>	vpair += vterm;
822	>	epot += (idat.sw) vterm;
823
824		a1 = 5.0 * ct_i * ct_j - ct_ij;
825
826	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
826	>	dVdr += preSw * three * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
827
828	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
829	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
828	>	duduz_i += preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
829	>	duduz_j += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_*uz_i);
830
831	+	if (idat.excluded) {
832	+	indirect_vpair += - pref * preRF2_ * ct_ij;
833	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
834	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
835	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
836	+	}
837	+
838		} else {
839
840		if (i_is_SplitDipole) {
841		if (j_is_SplitDipole) {
842	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
842	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
843		} else {
844	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
844	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
845		}
846		ri = 1.0 / BigR;
847	<	scale = idat.rij * ri;
847	>	scale = (idat.rij) ri;
848		} else {
849		if (j_is_SplitDipole) {
850	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
850	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
851		ri = 1.0 / BigR;
852	<	scale = idat.rij * ri;
852	>	scale = (idat.rij) ri;
853		} else {
854		ri = riji;
855		scale = 1.0;
#	Line 729 \| Line 857 \| namespace OpenMD {
857		}
858		if (screeningMethod_ == DAMPED) {
859		// assemble damping variables
860	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
861	<	erfcVal = res.first;
862	<	derfcVal = res.second;
860	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
861	>	//erfcVal = res.first;
862	>	//derfcVal = res.second;
863	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
864	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
865		c1 = erfcVal * ri;
866		c2 = (-derfcVal + c1) * ri;
867		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 751 \| Line 881 \| namespace OpenMD {
881		preSwSc = preSw * scale;
882		c2ri = c2 * ri;
883		c3ri = c3 * ri;
884	<	c4rij = c4 * idat.rij;
884	>	c4rij = c4 * *(idat.rij) ;
885
886		// calculate the potential
887		pot_term = (ct_ij * c2ri - ctidotj * c3);
888		vterm = pref * pot_term;
889	<	idat.vpair += vterm;
890	<	epot += idat.sw * vterm;
889	>	vpair += vterm;
890	>	epot += (idat.sw) vterm;
891
892		// calculate derivatives for the forces and torques
893		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 776 \| Line 906 \| namespace OpenMD {
906		cy2 = cy_i * cy_i;
907		cz2 = cz_i * cz_i;
908
909	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
909	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
910
911		if (screeningMethod_ == DAMPED) {
912		// assemble the damping variables
913	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
914	<	erfcVal = res.first;
915	<	derfcVal = res.second;
913	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
914	>	//erfcVal = res.first;
915	>	//derfcVal = res.second;
916	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
917	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
918		c1 = erfcVal * riji;
919		c2 = (-derfcVal + c1) * riji;
920		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 795 \| Line 927 \| namespace OpenMD {
927		}
928
929		// precompute some variables for convenience
930	<	preSw = idat.sw * pref;
930	>	preSw = (idat.sw) pref;
931		c2ri = c2 * riji;
932		c3ri = c3 * riji;
933	<	c4rij = c4 * idat.rij;
934	<	rhatdot2 = 2.0 * rhat * c3;
933	>	c4rij = c4 * *(idat.rij) ;
934	>	rhatdot2 = two * rhat * c3;
935		rhatc4 = rhat * c4rij;
936
937		// calculate the potential
#	Line 808 \| Line 940 \| namespace OpenMD {
940		qzz_i * (cz2 * c3 - c2ri) );
941
942		vterm = pref * pot_term;
943	<	idat.vpair += vterm;
944	<	epot += idat.sw * vterm;
943	>	vpair += vterm;
944	>	epot += (idat.sw) vterm;
945
946		// calculate the derivatives for the forces and torques
947
948	<	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (2.0cx_iux_i + rhat)c3ri) +
949	<	qyy_i* (cy2rhatc4 - (2.0cy_iuy_i + rhat)c3ri) +
950	<	qzz_i* (cz2rhatc4 - (2.0cz_iuz_i + rhat)c3ri));
948	>	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (twocx_iux_i + rhat)c3ri) +
949	>	qyy_i* (cy2rhatc4 - (twocy_iuy_i + rhat)c3ri) +
950	>	qzz_i* (cz2rhatc4 - (twocz_iuz_i + rhat)c3ri));
951
952		dudux_i += preSw * qxx_i * cx_i * rhatdot2;
953		duduy_i += preSw * qyy_i * cy_i * rhatdot2;
#	Line 823 \| Line 955 \| namespace OpenMD {
955		}
956		}
957
826	–	idat.pot += epot;
827	–	idat.f1 += dVdr;
958
959	<	if (i_is_Dipole \|\| i_is_Quadrupole)
960	<	idat.t1 -= cross(uz_i, duduz_i);
961	<	if (i_is_Quadrupole) {
962	<	idat.t1 -= cross(ux_i, dudux_i);
963	<	idat.t1 -= cross(uy_i, duduy_i);
964	<	}
959	>	if (!idat.excluded) {
960	>	*(idat.vpair) += vpair;
961	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
962	>	*(idat.f1) += dVdr;
963	>
964	>	if (i_is_Dipole \|\| i_is_Quadrupole)
965	>	*(idat.t1) -= cross(uz_i, duduz_i);
966	>	if (i_is_Quadrupole) {
967	>	*(idat.t1) -= cross(ux_i, dudux_i);
968	>	*(idat.t1) -= cross(uy_i, duduy_i);
969	>	}
970	>
971	>	if (j_is_Dipole \|\| j_is_Quadrupole)
972	>	*(idat.t2) -= cross(uz_j, duduz_j);
973	>	if (j_is_Quadrupole) {
974	>	*(idat.t2) -= cross(uz_j, dudux_j);
975	>	*(idat.t2) -= cross(uz_j, duduy_j);
976	>	}
977
978	<	if (j_is_Dipole \|\| j_is_Quadrupole)
837	<	idat.t2 -= cross(uz_j, duduz_j);
838	<	if (j_is_Quadrupole) {
839	<	idat.t2 -= cross(uz_j, dudux_j);
840	<	idat.t2 -= cross(uz_j, duduy_j);
841	<	}
978	>	} else {
979
980	<	return;
981	<	}
980	>	// only accumulate the forces and torques resulting from the
981	>	// indirect reaction field terms.
982
983	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
984	<
985	<	if (!initialized_) initialize();
849	<
850	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
851	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
852	<
853	<	// logicals
854	<
855	<	bool i_is_Charge = data1.is_Charge;
856	<	bool i_is_Dipole = data1.is_Dipole;
857	<
858	<	bool j_is_Charge = data2.is_Charge;
859	<	bool j_is_Dipole = data2.is_Dipole;
860	<
861	<	RealType q_i, q_j;
862	<
863	<	// The skippedCharge computation is needed by the real-space cutoff methods
864	<	// (i.e. shifted force and shifted potential)
865	<
866	<	if (i_is_Charge) {
867	<	q_i = data1.charge;
868	<	skdat.skippedCharge2 += q_i;
869	<	}
870	<
871	<	if (j_is_Charge) {
872	<	q_j = data2.charge;
873	<	skdat.skippedCharge1 += q_j;
874	<	}
875	<
876	<	// the rest of this function should only be necessary for reaction field.
877	<
878	<	if (summationMethod_ == REACTION_FIELD) {
879	<	RealType riji, ri2, ri3;
880	<	RealType q_i, mu_i, ct_i;
881	<	RealType q_j, mu_j, ct_j;
882	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
883	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
884	<
885	<	// some variables we'll need independent of electrostatic type:
983	>	*(idat.vpair) += indirect_vpair;
984	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
985	>	*(idat.f1) += indirect_dVdr;
986
887	–	riji = 1.0 / skdat.rij;
888	–	rhat = skdat.d * riji;
889	–
890	–	if (i_is_Dipole) {
891	–	mu_i = data1.dipole_moment;
892	–	uz_i = skdat.eFrame1.getColumn(2);
893	–	ct_i = dot(uz_i, rhat);
894	–	duduz_i = V3Zero;
895	–	}
896	–
897	–	if (j_is_Dipole) {
898	–	mu_j = data2.dipole_moment;
899	–	uz_j = skdat.eFrame2.getColumn(2);
900	–	ct_j = dot(uz_j, rhat);
901	–	duduz_j = V3Zero;
902	–	}
903	–
904	–	if (i_is_Charge) {
905	–	if (j_is_Charge) {
906	–	preVal = skdat.electroMult * pre11_ * q_i * q_j;
907	–	rfVal = preRF_ * skdat.rij * skdat.rij;
908	–	vterm = preVal * rfVal;
909	–	myPot += skdat.sw * vterm;
910	–	dudr = skdat.sw * preVal * 2.0 * rfVal * riji;
911	–	dVdr += dudr * rhat;
912	–	}
913	–
914	–	if (j_is_Dipole) {
915	–	ri2 = riji * riji;
916	–	ri3 = ri2 * riji;
917	–	pref = skdat.electroMult * pre12_ * q_i * mu_j;
918	–	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
919	–	myPot += skdat.sw * vterm;
920	–	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
921	–	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
922	–	}
923	–	}
924	–	if (i_is_Dipole) {
925	–	if (j_is_Charge) {
926	–	ri2 = riji * riji;
927	–	ri3 = ri2 * riji;
928	–	pref = skdat.electroMult * pre12_ * q_j * mu_i;
929	–	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
930	–	myPot += skdat.sw * vterm;
931	–	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
932	–	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
933	–	}
934	–	}
935	–
936	–	// accumulate the forces and torques resulting from the self term
937	–	skdat.pot += myPot;
938	–	skdat.f1 += dVdr;
939	–
987		if (i_is_Dipole)
988	<	skdat.t1 -= cross(uz_i, duduz_i);
988	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
989		if (j_is_Dipole)
990	<	skdat.t2 -= cross(uz_j, duduz_j);
990	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
991		}
992	<	}
992	>
993	>
994	>	return;
995	>	}
996
997	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
997	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
998		RealType mu1, preVal, chg1, self;
999
1000		if (!initialized_) initialize();
1001	<
1002	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1001	>
1002	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1003
1004		// logicals
955	–
1005		bool i_is_Charge = data.is_Charge;
1006		bool i_is_Dipole = data.is_Dipole;
1007
1008	<	if (summationMethod_ == REACTION_FIELD) {
1008	>	if (summationMethod_ == esm_REACTION_FIELD) {
1009		if (i_is_Dipole) {
1010		mu1 = data.dipole_moment;
1011		preVal = pre22_ * preRF2_ * mu1 * mu1;
1012	<	scdat.pot -= 0.5 * preVal;
1012	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1013
1014		// The self-correction term adds into the reaction field vector
1015	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1015	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1016		Vector3d ei = preVal * uz_i;
1017
1018		// This looks very wrong. A vector crossed with itself is zero.
1019	<	scdat.t -= cross(uz_i, ei);
1019	>	*(sdat.t) -= cross(uz_i, ei);
1020		}
1021	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1021	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1022		if (i_is_Charge) {
1023		chg1 = data.charge;
1024		if (screeningMethod_ == DAMPED) {
1025	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1025	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1026		} else {
1027	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1027	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1028		}
1029	<	scdat.pot += self;
1029	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1030		}
1031		}
1032		}
1033
1034	<	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1034	>	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1035		// This seems to work moderately well as a default. There's no
1036		// inherent scale for 1/r interactions that we can standardize.
1037		// 12 angstroms seems to be a reasonably good guess for most

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Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents): Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs. Revision 1718 by gezelter, Thu May 24 01:29:59 2012 UTC

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Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1718 by gezelter, Thu May 24 01:29:59 2012 UTC