[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 1720 by gezelter, Thu May 24 01:48:29 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
57
58		namespace OpenMD {
59
60		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
61	<	forceField_(NULL) {}
61	>	forceField_(NULL), info_(NULL),
62	>	haveCutoffRadius_(false),
63	>	haveDampingAlpha_(false),
64	>	haveDielectric_(false),
65	>	haveElectroSpline_(false)
66	>	{}
67
68		void Electrostatic::initialize() {
69	+
70	+	Globals* simParams_ = info_->getSimParams();
71	+
72	+	summationMap_["HARD"] = esm_HARD;
73	+	summationMap_["NONE"] = esm_HARD;
74	+	summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
75	+	summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL;
76	+	summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE;
77	+	summationMap_["REACTION_FIELD"] = esm_REACTION_FIELD;
78	+	summationMap_["EWALD_FULL"] = esm_EWALD_FULL;
79	+	summationMap_["EWALD_PME"] = esm_EWALD_PME;
80	+	summationMap_["EWALD_SPME"] = esm_EWALD_SPME;
81	+	screeningMap_["DAMPED"] = DAMPED;
82	+	screeningMap_["UNDAMPED"] = UNDAMPED;
83	+
84		// these prefactors convert the multipole interactions into kcal / mol
85		// all were computed assuming distances are measured in angstroms
86		// Charge-Charge, assuming charges are measured in electrons
#	Line 79 \| Line 105 \| namespace OpenMD {
105
106		// variables to handle different summation methods for long-range
107		// electrostatics:
108	<	summationMethod_ = NONE;
108	>	summationMethod_ = esm_HARD;
109		screeningMethod_ = UNDAMPED;
110		dielectric_ = 1.0;
111		one_third_ = 1.0 / 3.0;
86	–	haveDefaultCutoff_ = false;
87	–	haveDampingAlpha_ = false;
88	–	haveDielectric_ = false;
89	–	haveElectroSpline_ = false;
112
113	+	// check the summation method:
114	+	if (simParams_->haveElectrostaticSummationMethod()) {
115	+	string myMethod = simParams_->getElectrostaticSummationMethod();
116	+	toUpper(myMethod);
117	+	map<string, ElectrostaticSummationMethod>::iterator i;
118	+	i = summationMap_.find(myMethod);
119	+	if ( i != summationMap_.end() ) {
120	+	summationMethod_ = (*i).second;
121	+	} else {
122	+	// throw error
123	+	sprintf( painCave.errMsg,
124	+	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
125	+	"\t(Input file specified %s .)\n"
126	+	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
127	+	"\t\"shifted_potential\", \"shifted_force\", or \n"
128	+	"\t\"reaction_field\".\n", myMethod.c_str() );
129	+	painCave.isFatal = 1;
130	+	simError();
131	+	}
132	+	} else {
133	+	// set ElectrostaticSummationMethod to the cutoffMethod:
134	+	if (simParams_->haveCutoffMethod()){
135	+	string myMethod = simParams_->getCutoffMethod();
136	+	toUpper(myMethod);
137	+	map<string, ElectrostaticSummationMethod>::iterator i;
138	+	i = summationMap_.find(myMethod);
139	+	if ( i != summationMap_.end() ) {
140	+	summationMethod_ = (*i).second;
141	+	}
142	+	}
143	+	}
144	+
145	+	if (summationMethod_ == esm_REACTION_FIELD) {
146	+	if (!simParams_->haveDielectric()) {
147	+	// throw warning
148	+	sprintf( painCave.errMsg,
149	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
150	+	"\tA default value of %f will be used for the dielectric.\n", dielectric_);
151	+	painCave.isFatal = 0;
152	+	painCave.severity = OPENMD_INFO;
153	+	simError();
154	+	} else {
155	+	dielectric_ = simParams_->getDielectric();
156	+	}
157	+	haveDielectric_ = true;
158	+	}
159	+
160	+	if (simParams_->haveElectrostaticScreeningMethod()) {
161	+	string myScreen = simParams_->getElectrostaticScreeningMethod();
162	+	toUpper(myScreen);
163	+	map<string, ElectrostaticScreeningMethod>::iterator i;
164	+	i = screeningMap_.find(myScreen);
165	+	if ( i != screeningMap_.end()) {
166	+	screeningMethod_ = (*i).second;
167	+	} else {
168	+	sprintf( painCave.errMsg,
169	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
170	+	"\t(Input file specified %s .)\n"
171	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
172	+	"or \"damped\".\n", myScreen.c_str() );
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	}
177	+
178	+	// check to make sure a cutoff value has been set:
179	+	if (!haveCutoffRadius_) {
180	+	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
181	+	"Cutoff value!\n");
182	+	painCave.severity = OPENMD_ERROR;
183	+	painCave.isFatal = 1;
184	+	simError();
185	+	}
186	+
187	+	if (screeningMethod_ == DAMPED) {
188	+	if (!simParams_->haveDampingAlpha()) {
189	+	// first set a cutoff dependent alpha value
190	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
191	+	dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
192	+	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
193	+
194	+	// throw warning
195	+	sprintf( painCave.errMsg,
196	+	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
197	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
198	+	dampingAlpha_, cutoffRadius_);
199	+	painCave.severity = OPENMD_INFO;
200	+	painCave.isFatal = 0;
201	+	simError();
202	+	} else {
203	+	dampingAlpha_ = simParams_->getDampingAlpha();
204	+	}
205	+	haveDampingAlpha_ = true;
206	+	}
207	+
208		// find all of the Electrostatic atom Types:
209		ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
210		ForceField::AtomTypeContainer::MapTypeIterator i;
211		AtomType* at;
212	<
212	>
213		for (at = atomTypes->beginType(i); at != NULL;
214		at = atomTypes->nextType(i)) {
215
#	Line 100 \| Line 217 \| namespace OpenMD {
217		addType(at);
218		}
219
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	–	}
220
221	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
222	<	rcuti_ = 1.0 / defaultCutoff_;
221	>	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
222	>	rcuti_ = 1.0 / cutoffRadius_;
223		rcuti2_ = rcuti_ * rcuti_;
224		rcuti3_ = rcuti2_ * rcuti_;
225		rcuti4_ = rcuti2_ * rcuti2_;
226
227		if (screeningMethod_ == DAMPED) {
228	<	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	<
228	>
229		alpha2_ = dampingAlpha_ * dampingAlpha_;
230		alpha4_ = alpha2_ * alpha2_;
231		alpha6_ = alpha4_ * alpha2_;
232		alpha8_ = alpha4_ * alpha4_;
233
234	<	constEXP_ = exp(-alpha2_ * defaultCutoff2_);
234	>	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
235		invRootPi_ = 0.56418958354775628695;
236		alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
237
238	<	c1c_ = erfc(dampingAlpha_ * defaultCutoff_) * rcuti_;
238	>	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
239		c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
240		c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
241		c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
#	Line 148 \| Line 250 \| namespace OpenMD {
250		c6c_ = 9.0 * c5c_ * rcuti2_;
251		}
252
253	<	if (summationMethod_ == REACTION_FIELD) {
254	<	if (haveDielectric_) {
255	<	preRF_ = (dielectric_ - 1.0) /
256	<	((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	<	}
253	>	if (summationMethod_ == esm_REACTION_FIELD) {
254	>	preRF_ = (dielectric_ - 1.0) /
255	>	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
256	>	preRF2_ = 2.0 * preRF_;
257		}
258	<
259	<	RealType dx = defaultCutoff_ / RealType(np_ - 1);
258	>
259	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
260	>	// have charged atoms longer than the cutoffRadius away from each
261	>	// other. Splining may not be the best choice here. Direct calls
262	>	// to erfc might be preferrable.
263	>
264	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
265		RealType rval;
266		vector<RealType> rvals;
267		vector<RealType> yvals;
#	Line 186 \| Line 285 \| namespace OpenMD {
285		electrostaticAtomData.is_SplitDipole = false;
286		electrostaticAtomData.is_Quadrupole = false;
287
288	<	if (atomType->isCharge()) {
190	<	GenericData* data = atomType->getPropertyByName("Charge");
288	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
289
290	<	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	<	}
290	>	if (fca.isFixedCharge()) {
291		electrostaticAtomData.is_Charge = true;
292	<	electrostaticAtomData.charge = doubleData->getData();
292	>	electrostaticAtomData.fixedCharge = fca.getCharge();
293		}
294
295	<	if (atomType->isDirectional()) {
296	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
297	<
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	<	}
295	>	MultipoleAdapter ma = MultipoleAdapter(atomType);
296	>	if (ma.isMultipole()) {
297	>	if (ma.isDipole()) {
298		electrostaticAtomData.is_Dipole = true;
299	<	electrostaticAtomData.dipole_moment = doubleData->getData();
299	>	electrostaticAtomData.dipole_moment = ma.getDipoleMoment();
300		}
301	<
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	<	}
301	>	if (ma.isSplitDipole()) {
302		electrostaticAtomData.is_SplitDipole = true;
303	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
303	>	electrostaticAtomData.split_dipole_distance = ma.getSplitDipoleDistance();
304		}
305	<
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	<
305	>	if (ma.isQuadrupole()) {
306		// Quadrupoles in OpenMD are set as the diagonal elements
307		// of the diagonalized traceless quadrupole moment tensor.
308		// The column vectors of the unitary matrix that diagonalizes
309		// the quadrupole moment tensor become the eFrame (or the
310		// 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	–	}
311		electrostaticAtomData.is_Quadrupole = true;
312	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
312	>	electrostaticAtomData.quadrupole_moments = ma.getQuadrupoleMoments();
313		}
314		}
315
316	<	AtomTypeProperties atp = atomType->getATP();
316	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
317
318	+	if (fqa.isFluctuatingCharge()) {
319	+	electrostaticAtomData.is_Fluctuating = true;
320	+	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
321	+	electrostaticAtomData.hardness = fqa.getHardness();
322	+	electrostaticAtomData.slaterN = fqa.getSlaterN();
323	+	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
324	+	}
325	+
326		pair<map<int,AtomType*>::iterator,bool> ret;
327	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
327	>	ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
328	>	atomType) );
329		if (ret.second == false) {
330		sprintf( painCave.errMsg,
331		"Electrostatic already had a previous entry with ident %d\n",
332	<	atp.ident);
332	>	atomType->getIdent() );
333		painCave.severity = OPENMD_INFO;
334		painCave.isFatal = 0;
335		simError();
336		}
337
338	<	ElectrostaticMap[atomType] = electrostaticAtomData;
338	>	ElectrostaticMap[atomType] = electrostaticAtomData;
339	>
340	>	// Now, iterate over all known types and add to the mixing map:
341	>
342	>	map<AtomType*, ElectrostaticAtomData>::iterator it;
343	>	for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
344	>	AtomType* atype2 = (*it).first;
345	>	ElectrostaticAtomData eaData2 = (*it).second;
346	>	if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) {
347	>
348	>	RealType a = electrostaticAtomData.slaterZeta;
349	>	RealType b = eaData2.slaterZeta;
350	>	int m = electrostaticAtomData.slaterN;
351	>	int n = eaData2.slaterN;
352	>
353	>	// Create the spline of the coulombic integral for s-type
354	>	// Slater orbitals. Add a 2 angstrom safety window to deal
355	>	// with cutoffGroups that have charged atoms longer than the
356	>	// cutoffRadius away from each other.
357	>
358	>	RealType rval;
359	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
360	>	vector<RealType> rvals;
361	>	vector<RealType> J1vals;
362	>	vector<RealType> J2vals;
363	>	for (int i = 0; i < np_; i++) {
364	>	rval = RealType(i) * dr;
365	>	rvals.push_back(rval);
366	>	J1vals.push_back( sSTOCoulInt( a, b, m, n, rval * PhysicalConstants::angstromsToBohr ) );
367	>	J2vals.push_back( sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) );
368	>	}
369	>
370	>	CubicSpline* J1 = new CubicSpline();
371	>	J1->addPoints(rvals, J1vals);
372	>	CubicSpline* J2 = new CubicSpline();
373	>	J2->addPoints(rvals, J2vals);
374	>
375	>	pair<AtomType, AtomType> key1, key2;
376	>	key1 = make_pair(atomType, atype2);
377	>	key2 = make_pair(atype2, atomType);
378	>
379	>	Jij[key1] = J1;
380	>	Jij[key2] = J2;
381	>	}
382	>	}
383	>
384		return;
385		}
386
387	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
388	<	RealType theRSW ) {
389	<	defaultCutoff_ = theECR;
390	<	rrf_ = defaultCutoff_;
328	<	rt_ = theRSW;
329	<	haveDefaultCutoff_ = true;
387	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
388	>	cutoffRadius_ = rCut;
389	>	rrf_ = cutoffRadius_;
390	>	haveCutoffRadius_ = true;
391		}
392	+
393	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
394	+	rt_ = rSwitch;
395	+	}
396		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
397		summationMethod_ = esm;
398		}
#	Line 343 \| Line 408 \| namespace OpenMD {
408		haveDielectric_ = true;
409		}
410
411	<	void Electrostatic::calcForce(InteractionData idat) {
411	>	void Electrostatic::calcForce(InteractionData &idat) {
412
413		// utility variables. Should clean these up and use the Vector3d and
414		// Mat3x3d to replace as many as we can in future versions:
#	Line 357 \| Line 422 \| namespace OpenMD {
422		RealType ct_i, ct_j, ct_ij, a1;
423		RealType riji, ri, ri2, ri3, ri4;
424		RealType pref, vterm, epot, dudr;
425	+	RealType vpair(0.0);
426		RealType scale, sc2;
427		RealType pot_term, preVal, rfVal;
428		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
429		RealType preSw, preSwSc;
430		RealType c1, c2, c3, c4;
431	<	RealType erfcVal, derfcVal;
431	>	RealType erfcVal(1.0), derfcVal(0.0);
432		RealType BigR;
433	+	RealType two(2.0), three(3.0);
434
435		Vector3d Q_i, Q_j;
436		Vector3d ux_i, uy_i, uz_i;
#	Line 373 \| Line 440 \| namespace OpenMD {
440		Vector3d rhatdot2, rhatc4;
441		Vector3d dVdr;
442
443	+	// variables for indirect (reaction field) interactions for excluded pairs:
444	+	RealType indirect_Pot(0.0);
445	+	RealType indirect_vpair(0.0);
446	+	Vector3d indirect_dVdr(V3Zero);
447	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
448	+
449		pair<RealType, RealType> res;
450
451		if (!initialized_) initialize();
452
453	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
454	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
453	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
454	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
455
456		// some variables we'll need independent of electrostatic type:
457
458	<	riji = 1.0 / idat.rij;
459	<	Vector3d rhat = idat.d * riji;
458	>	riji = 1.0 / *(idat.rij) ;
459	>	Vector3d rhat = (idat.d) riji;
460
461		// logicals
462
#	Line 397 \| Line 470 \| namespace OpenMD {
470		bool j_is_SplitDipole = data2.is_SplitDipole;
471		bool j_is_Quadrupole = data2.is_Quadrupole;
472
473	<	if (i_is_Charge)
474	<	q_i = data1.charge;
473	>	if (i_is_Charge) {
474	>	q_i = data1.fixedCharge;
475	>	if (idat.excluded) {
476	>	*(idat.skippedCharge2) += q_i;
477	>	}
478	>	}
479
480		if (i_is_Dipole) {
481		mu_i = data1.dipole_moment;
482	<	uz_i = idat.eFrame1.getColumn(2);
482	>	uz_i = idat.eFrame1->getColumn(2);
483
484		ct_i = dot(uz_i, rhat);
485
#	Line 418 \| Line 495 \| namespace OpenMD {
495		qyy_i = Q_i.y();
496		qzz_i = Q_i.z();
497
498	<	ux_i = idat.eFrame1.getColumn(0);
499	<	uy_i = idat.eFrame1.getColumn(1);
500	<	uz_i = idat.eFrame1.getColumn(2);
498	>	ux_i = idat.eFrame1->getColumn(0);
499	>	uy_i = idat.eFrame1->getColumn(1);
500	>	uz_i = idat.eFrame1->getColumn(2);
501
502		cx_i = dot(ux_i, rhat);
503		cy_i = dot(uy_i, rhat);
#	Line 431 \| Line 508 \| namespace OpenMD {
508		duduz_i = V3Zero;
509		}
510
511	<	if (j_is_Charge)
512	<	q_j = data2.charge;
511	>	if (j_is_Charge) {
512	>	q_j = data2.fixedCharge;
513	>	if (idat.excluded) {
514	>	*(idat.skippedCharge1) += q_j;
515	>	}
516	>	}
517
518	+
519		if (j_is_Dipole) {
520		mu_j = data2.dipole_moment;
521	<	uz_j = idat.eFrame2.getColumn(2);
521	>	uz_j = idat.eFrame2->getColumn(2);
522
523		ct_j = dot(uz_j, rhat);
524
#	Line 452 \| Line 534 \| namespace OpenMD {
534		qyy_j = Q_j.y();
535		qzz_j = Q_j.z();
536
537	<	ux_j = idat.eFrame2.getColumn(0);
538	<	uy_j = idat.eFrame2.getColumn(1);
539	<	uz_j = idat.eFrame2.getColumn(2);
537	>	ux_j = idat.eFrame2->getColumn(0);
538	>	uy_j = idat.eFrame2->getColumn(1);
539	>	uz_j = idat.eFrame2->getColumn(2);
540
541		cx_j = dot(ux_j, rhat);
542		cy_j = dot(uy_j, rhat);
#	Line 473 \| Line 555 \| namespace OpenMD {
555		if (j_is_Charge) {
556		if (screeningMethod_ == DAMPED) {
557		// assemble the damping variables
558	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
559	<	erfcVal = res.first;
560	<	derfcVal = res.second;
558	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
559	>	//erfcVal = res.first;
560	>	//derfcVal = res.second;
561	>
562	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
563	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
564	>
565		c1 = erfcVal * riji;
566		c2 = (-derfcVal + c1) * riji;
567		} else {
#	Line 483 \| Line 569 \| namespace OpenMD {
569		c2 = c1 * riji;
570		}
571
572	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
572	>	preVal = (idat.electroMult) pre11_ * q_i * q_j;
573
574	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
574	>	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
575		vterm = preVal * (c1 - c1c_);
576	<	dudr = -idat.sw * preVal * c2;
576	>	dudr = - (idat.sw) preVal * c2;
577
578	<	} else if (summationMethod_ == SHIFTED_FORCE) {
579	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
580	<	dudr = idat.sw * preVal * (c2c_ - c2);
578	>	} else if (summationMethod_ == esm_SHIFTED_FORCE) {
579	>	vterm = preVal * ( c1 - c1c_ + c2c_( (idat.rij) - cutoffRadius_) );
580	>	dudr = (idat.sw) preVal * (c2c_ - c2);
581
582	<	} else if (summationMethod_ == REACTION_FIELD) {
583	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
582	>	} else if (summationMethod_ == esm_REACTION_FIELD) {
583	>	rfVal = preRF_ * (idat.rij) *(idat.rij);
584	>
585		vterm = preVal * ( riji + rfVal );
586	<	dudr = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
586	>	dudr = (idat.sw) preVal * ( 2.0 * rfVal - riji ) * riji;
587	>
588	>	// if this is an excluded pair, there are still indirect
589	>	// interactions via the reaction field we must worry about:
590
591	+	if (idat.excluded) {
592	+	indirect_vpair += preVal * rfVal;
593	+	indirect_Pot += (idat.sw) preVal * rfVal;
594	+	indirect_dVdr += (idat.sw) preVal * two * rfVal * riji * rhat;
595	+	}
596	+
597		} else {
502	–	vterm = preVal * riji * erfcVal;
598
599	<	dudr = - idat.sw * preVal * c2;
599	>	vterm = preVal * riji * erfcVal;
600	>	dudr = - (idat.sw) preVal * c2;
601
602		}
507	–
508	–	idat.vpair += vterm;
509	–	epot += idat.sw * vterm;
603
604	<	dVdr += dudr * rhat;
604	>	vpair += vterm;
605	>	epot += (idat.sw) vterm;
606	>	dVdr += dudr * rhat;
607		}
608
609		if (j_is_Dipole) {
610		// pref is used by all the possible methods
611	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
612	<	preSw = idat.sw * pref;
611	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
612	>	preSw = (idat.sw) pref;
613
614	<	if (summationMethod_ == REACTION_FIELD) {
614	>	if (summationMethod_ == esm_REACTION_FIELD) {
615		ri2 = riji * riji;
616		ri3 = ri2 * riji;
617
618	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
619	<	idat.vpair += vterm;
620	<	epot += idat.sw * vterm;
618	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
619	>	vpair += vterm;
620	>	epot += (idat.sw) vterm;
621
622	<	dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
623	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
622	>	dVdr += -preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
623	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
624
625	+	// Even if we excluded this pair from direct interactions,
626	+	// we still have the reaction-field-mediated charge-dipole
627	+	// interaction:
628	+
629	+	if (idat.excluded) {
630	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
631	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
632	+	indirect_dVdr += preSw * preRF2_ * uz_j;
633	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
634	+	}
635	+
636		} else {
637		// determine the inverse r used if we have split dipoles
638		if (j_is_SplitDipole) {
639	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
639	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
640		ri = 1.0 / BigR;
641	<	scale = idat.rij * ri;
641	>	scale = (idat.rij) ri;
642		} else {
643		ri = riji;
644		scale = 1.0;
#	Line 542 \| Line 648 \| namespace OpenMD {
648
649		if (screeningMethod_ == DAMPED) {
650		// assemble the damping variables
651	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
652	<	erfcVal = res.first;
653	<	derfcVal = res.second;
651	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
652	>	//erfcVal = res.first;
653	>	//derfcVal = res.second;
654	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
655	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
656		c1 = erfcVal * ri;
657		c2 = (-derfcVal + c1) * ri;
658		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 559 \| Line 667 \| namespace OpenMD {
667		// calculate the potential
668		pot_term = scale * c2;
669		vterm = -pref * ct_j * pot_term;
670	<	idat.vpair += vterm;
671	<	epot += idat.sw * vterm;
670	>	vpair += vterm;
671	>	epot += (idat.sw) vterm;
672
673		// calculate derivatives for forces and torques
674
#	Line 575 \| Line 683 \| namespace OpenMD {
683		cx2 = cx_j * cx_j;
684		cy2 = cy_j * cy_j;
685		cz2 = cz_j * cz_j;
686	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
686	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
687
688		if (screeningMethod_ == DAMPED) {
689		// assemble the damping variables
690	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
691	<	erfcVal = res.first;
692	<	derfcVal = res.second;
690	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
691	>	//erfcVal = res.first;
692	>	//derfcVal = res.second;
693	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
694	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
695		c1 = erfcVal * riji;
696		c2 = (-derfcVal + c1) * riji;
697		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 594 \| Line 704 \| namespace OpenMD {
704		}
705
706		// precompute variables for convenience
707	<	preSw = idat.sw * pref;
707	>	preSw = (idat.sw) pref;
708		c2ri = c2 * riji;
709		c3ri = c3 * riji;
710	<	c4rij = c4 * idat.rij;
711	<	rhatdot2 = 2.0 * rhat * c3;
710	>	c4rij = c4 * *(idat.rij) ;
711	>	rhatdot2 = two * rhat * c3;
712		rhatc4 = rhat * c4rij;
713
714		// calculate the potential
#	Line 606 \| Line 716 \| namespace OpenMD {
716		qyy_j * (cy2*c3 - c2ri) +
717		qzz_j * (cz2*c3 - c2ri) );
718		vterm = pref * pot_term;
719	<	idat.vpair += vterm;
720	<	epot += idat.sw * vterm;
719	>	vpair += vterm;
720	>	epot += (idat.sw) vterm;
721
722		// calculate derivatives for the forces and torques
723
724	<	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (2.0cx_jux_j + rhat)c3ri) +
725	<	qyy_j* (cy2rhatc4 - (2.0cy_juy_j + rhat)c3ri) +
726	<	qzz_j* (cz2rhatc4 - (2.0cz_juz_j + rhat)c3ri));
724	>	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (twocx_jux_j + rhat)c3ri) +
725	>	qyy_j* (cy2rhatc4 - (twocy_juy_j + rhat)c3ri) +
726	>	qzz_j* (cz2rhatc4 - (twocz_juz_j + rhat)c3ri));
727
728		dudux_j += preSw * qxx_j * cx_j * rhatdot2;
729		duduy_j += preSw * qyy_j * cy_j * rhatdot2;
#	Line 625 \| Line 735 \| namespace OpenMD {
735
736		if (j_is_Charge) {
737		// variables used by all the methods
738	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
739	<	preSw = idat.sw * pref;
738	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
739	>	preSw = (idat.sw) pref;
740
741	<	if (summationMethod_ == REACTION_FIELD) {
741	>	if (summationMethod_ == esm_REACTION_FIELD) {
742
743		ri2 = riji * riji;
744		ri3 = ri2 * riji;
745
746	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
747	<	idat.vpair += vterm;
748	<	epot += idat.sw * vterm;
746	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
747	>	vpair += vterm;
748	>	epot += (idat.sw) vterm;
749
750	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
750	>	dVdr += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_ * uz_i);
751
752	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
752	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
753	>
754	>	// Even if we excluded this pair from direct interactions,
755	>	// we still have the reaction-field-mediated charge-dipole
756	>	// interaction:
757	>
758	>	if (idat.excluded) {
759	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
760	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
761	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
762	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
763	>	}
764
765		} else {
766
767		// determine inverse r if we are using split dipoles
768		if (i_is_SplitDipole) {
769	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
769	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
770		ri = 1.0 / BigR;
771	<	scale = idat.rij * ri;
771	>	scale = (idat.rij) ri;
772		} else {
773		ri = riji;
774		scale = 1.0;
#	Line 657 \| Line 778 \| namespace OpenMD {
778
779		if (screeningMethod_ == DAMPED) {
780		// assemble the damping variables
781	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
782	<	erfcVal = res.first;
783	<	derfcVal = res.second;
781	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
782	>	//erfcVal = res.first;
783	>	//derfcVal = res.second;
784	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
785	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
786		c1 = erfcVal * ri;
787		c2 = (-derfcVal + c1) * ri;
788		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 674 \| Line 797 \| namespace OpenMD {
797		// calculate the potential
798		pot_term = c2 * scale;
799		vterm = pref * ct_i * pot_term;
800	<	idat.vpair += vterm;
801	<	epot += idat.sw * vterm;
800	>	vpair += vterm;
801	>	epot += (idat.sw) vterm;
802
803		// calculate derivatives for the forces and torques
804		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
#	Line 687 \| Line 810 \| namespace OpenMD {
810		// variables used by all methods
811		ct_ij = dot(uz_i, uz_j);
812
813	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
814	<	preSw = idat.sw * pref;
813	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
814	>	preSw = (idat.sw) pref;
815
816	<	if (summationMethod_ == REACTION_FIELD) {
816	>	if (summationMethod_ == esm_REACTION_FIELD) {
817		ri2 = riji * riji;
818		ri3 = ri2 * riji;
819		ri4 = ri2 * ri2;
820
821		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
822		preRF2_ * ct_ij );
823	<	idat.vpair += vterm;
824	<	epot += idat.sw * vterm;
823	>	vpair += vterm;
824	>	epot += (idat.sw) vterm;
825
826		a1 = 5.0 * ct_i * ct_j - ct_ij;
827
828	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
828	>	dVdr += preSw * three * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
829
830	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
831	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
830	>	duduz_i += preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
831	>	duduz_j += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_*uz_i);
832
833	+	if (idat.excluded) {
834	+	indirect_vpair += - pref * preRF2_ * ct_ij;
835	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
836	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
837	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
838	+	}
839	+
840		} else {
841
842		if (i_is_SplitDipole) {
843		if (j_is_SplitDipole) {
844	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
844	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
845		} else {
846	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
846	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
847		}
848		ri = 1.0 / BigR;
849	<	scale = idat.rij * ri;
849	>	scale = (idat.rij) ri;
850		} else {
851		if (j_is_SplitDipole) {
852	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
852	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
853		ri = 1.0 / BigR;
854	<	scale = idat.rij * ri;
854	>	scale = (idat.rij) ri;
855		} else {
856		ri = riji;
857		scale = 1.0;
#	Line 729 \| Line 859 \| namespace OpenMD {
859		}
860		if (screeningMethod_ == DAMPED) {
861		// assemble damping variables
862	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
863	<	erfcVal = res.first;
864	<	derfcVal = res.second;
862	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
863	>	//erfcVal = res.first;
864	>	//derfcVal = res.second;
865	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
866	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
867		c1 = erfcVal * ri;
868		c2 = (-derfcVal + c1) * ri;
869		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 751 \| Line 883 \| namespace OpenMD {
883		preSwSc = preSw * scale;
884		c2ri = c2 * ri;
885		c3ri = c3 * ri;
886	<	c4rij = c4 * idat.rij;
886	>	c4rij = c4 * *(idat.rij) ;
887
888		// calculate the potential
889		pot_term = (ct_ij * c2ri - ctidotj * c3);
890		vterm = pref * pot_term;
891	<	idat.vpair += vterm;
892	<	epot += idat.sw * vterm;
891	>	vpair += vterm;
892	>	epot += (idat.sw) vterm;
893
894		// calculate derivatives for the forces and torques
895		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 776 \| Line 908 \| namespace OpenMD {
908		cy2 = cy_i * cy_i;
909		cz2 = cz_i * cz_i;
910
911	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
911	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
912
913		if (screeningMethod_ == DAMPED) {
914		// assemble the damping variables
915	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
916	<	erfcVal = res.first;
917	<	derfcVal = res.second;
915	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
916	>	//erfcVal = res.first;
917	>	//derfcVal = res.second;
918	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
919	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
920		c1 = erfcVal * riji;
921		c2 = (-derfcVal + c1) * riji;
922		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 795 \| Line 929 \| namespace OpenMD {
929		}
930
931		// precompute some variables for convenience
932	<	preSw = idat.sw * pref;
932	>	preSw = (idat.sw) pref;
933		c2ri = c2 * riji;
934		c3ri = c3 * riji;
935	<	c4rij = c4 * idat.rij;
936	<	rhatdot2 = 2.0 * rhat * c3;
935	>	c4rij = c4 * *(idat.rij) ;
936	>	rhatdot2 = two * rhat * c3;
937		rhatc4 = rhat * c4rij;
938
939		// calculate the potential
#	Line 808 \| Line 942 \| namespace OpenMD {
942		qzz_i * (cz2 * c3 - c2ri) );
943
944		vterm = pref * pot_term;
945	<	idat.vpair += vterm;
946	<	epot += idat.sw * vterm;
945	>	vpair += vterm;
946	>	epot += (idat.sw) vterm;
947
948		// calculate the derivatives for the forces and torques
949
950	<	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (2.0cx_iux_i + rhat)c3ri) +
951	<	qyy_i* (cy2rhatc4 - (2.0cy_iuy_i + rhat)c3ri) +
952	<	qzz_i* (cz2rhatc4 - (2.0cz_iuz_i + rhat)c3ri));
950	>	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (twocx_iux_i + rhat)c3ri) +
951	>	qyy_i* (cy2rhatc4 - (twocy_iuy_i + rhat)c3ri) +
952	>	qzz_i* (cz2rhatc4 - (twocz_iuz_i + rhat)c3ri));
953
954		dudux_i += preSw * qxx_i * cx_i * rhatdot2;
955		duduy_i += preSw * qyy_i * cy_i * rhatdot2;
#	Line 823 \| Line 957 \| namespace OpenMD {
957		}
958		}
959
826	–	idat.pot += epot;
827	–	idat.f1 += dVdr;
960
961	<	if (i_is_Dipole \|\| i_is_Quadrupole)
962	<	idat.t1 -= cross(uz_i, duduz_i);
963	<	if (i_is_Quadrupole) {
964	<	idat.t1 -= cross(ux_i, dudux_i);
965	<	idat.t1 -= cross(uy_i, duduy_i);
966	<	}
961	>	if (!idat.excluded) {
962	>	*(idat.vpair) += vpair;
963	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
964	>	*(idat.f1) += dVdr;
965	>
966	>	if (i_is_Dipole \|\| i_is_Quadrupole)
967	>	*(idat.t1) -= cross(uz_i, duduz_i);
968	>	if (i_is_Quadrupole) {
969	>	*(idat.t1) -= cross(ux_i, dudux_i);
970	>	*(idat.t1) -= cross(uy_i, duduy_i);
971	>	}
972	>
973	>	if (j_is_Dipole \|\| j_is_Quadrupole)
974	>	*(idat.t2) -= cross(uz_j, duduz_j);
975	>	if (j_is_Quadrupole) {
976	>	*(idat.t2) -= cross(uz_j, dudux_j);
977	>	*(idat.t2) -= cross(uz_j, duduy_j);
978	>	}
979
980	<	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	<	}
980	>	} else {
981
982	<	return;
983	<	}
982	>	// only accumulate the forces and torques resulting from the
983	>	// indirect reaction field terms.
984
985	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
986	<
987	<	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:
985	>	*(idat.vpair) += indirect_vpair;
986	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
987	>	*(idat.f1) += indirect_dVdr;
988
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	–
989		if (i_is_Dipole)
990	<	skdat.t1 -= cross(uz_i, duduz_i);
990	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
991		if (j_is_Dipole)
992	<	skdat.t2 -= cross(uz_j, duduz_j);
992	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
993		}
994	<	}
994	>
995	>
996	>	return;
997	>	}
998
999	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
999	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1000		RealType mu1, preVal, chg1, self;
1001
1002		if (!initialized_) initialize();
1003	<
1004	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1003	>
1004	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1005
1006		// logicals
955	–
1007		bool i_is_Charge = data.is_Charge;
1008		bool i_is_Dipole = data.is_Dipole;
1009
1010	<	if (summationMethod_ == REACTION_FIELD) {
1010	>	if (summationMethod_ == esm_REACTION_FIELD) {
1011		if (i_is_Dipole) {
1012		mu1 = data.dipole_moment;
1013		preVal = pre22_ * preRF2_ * mu1 * mu1;
1014	<	scdat.pot -= 0.5 * preVal;
1014	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1015
1016		// The self-correction term adds into the reaction field vector
1017	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1017	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1018		Vector3d ei = preVal * uz_i;
1019
1020		// This looks very wrong. A vector crossed with itself is zero.
1021	<	scdat.t -= cross(uz_i, ei);
1021	>	*(sdat.t) -= cross(uz_i, ei);
1022		}
1023	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1023	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1024		if (i_is_Charge) {
1025	<	chg1 = data.charge;
1025	>	chg1 = data.fixedCharge;
1026		if (screeningMethod_ == DAMPED) {
1027	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1027	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1028		} else {
1029	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1029	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1030		}
1031	<	scdat.pot += self;
1031	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1032		}
1033		}
1034		}
1035
1036	<	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1036	>	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1037		// This seems to work moderately well as a default. There's no
1038		// inherent scale for 1/r interactions that we can standardize.
1039		// 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 1720 by gezelter, Thu May 24 01:48:29 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 1720 by gezelter, Thu May 24 01:48:29 2012 UTC