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

Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1504 by gezelter, Sat Oct 2 20:41:53 2010 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 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
220	<	// check to make sure a cutoff value has been set:
221	<	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	<	}
111	<
112	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
113	<	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 185 \| Line 283 \| namespace OpenMD {
283		electrostaticAtomData.is_Dipole = false;
284		electrostaticAtomData.is_SplitDipole = false;
285		electrostaticAtomData.is_Quadrupole = false;
286	+	electrostaticAtomData.is_Fluctuating = 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	<
306	<	if (daType->isQuadrupole()) {
307	<	GenericData* data = daType->getPropertyByName("QuadrupoleMoments");
308	<
309	<	if (data == NULL) {
310	<	sprintf( painCave.errMsg,
278	<	"Electrostatic::addType could not find QuadrupoleMoments\n"
279	<	"\tparameter for atomType %s.\n",
280	<	daType->getName().c_str());
281	<	painCave.severity = OPENMD_ERROR;
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<
286	<	Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
287	<	if (v3dData == NULL) {
288	<	sprintf( painCave.errMsg,
289	<	"Electrostatic::addType could not convert GenericData to "
290	<	"Quadrupole Moments for\n"
291	<	"\tatom type %s\n", daType->getName().c_str());
292	<	painCave.severity = OPENMD_ERROR;
293	<	painCave.isFatal = 1;
294	<	simError();
295	<	}
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.
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	>	// may not be necessary if Slater coulomb integral is symmetric
368	>	J2vals.push_back( sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) );
369	>	}
370	>
371	>	CubicSpline* J1 = new CubicSpline();
372	>	J1->addPoints(rvals, J1vals);
373	>	CubicSpline* J2 = new CubicSpline();
374	>	J2->addPoints(rvals, J2vals);
375	>
376	>	pair<AtomType, AtomType> key1, key2;
377	>	key1 = make_pair(atomType, atype2);
378	>	key2 = make_pair(atype2, atomType);
379	>
380	>	Jij[key1] = J1;
381	>	Jij[key2] = J2;
382	>	}
383	>	}
384	>
385		return;
386		}
387
388	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
389	<	RealType theRSW ) {
390	<	defaultCutoff_ = theECR;
391	<	rrf_ = defaultCutoff_;
322	<	rt_ = theRSW;
323	<	haveDefaultCutoff_ = true;
388	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
389	>	cutoffRadius_ = rCut;
390	>	rrf_ = cutoffRadius_;
391	>	haveCutoffRadius_ = true;
392		}
393	+
394	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
395	+	rt_ = rSwitch;
396	+	}
397		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
398		summationMethod_ = esm;
399		}
#	Line 337 \| Line 409 \| namespace OpenMD {
409		haveDielectric_ = true;
410		}
411
412	<	void Electrostatic::calcForce(InteractionData idat) {
412	>	void Electrostatic::calcForce(InteractionData &idat) {
413
414		// utility variables. Should clean these up and use the Vector3d and
415		// Mat3x3d to replace as many as we can in future versions:
#	Line 351 \| Line 423 \| namespace OpenMD {
423		RealType ct_i, ct_j, ct_ij, a1;
424		RealType riji, ri, ri2, ri3, ri4;
425		RealType pref, vterm, epot, dudr;
426	+	RealType vpair(0.0);
427		RealType scale, sc2;
428		RealType pot_term, preVal, rfVal;
429		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
430		RealType preSw, preSwSc;
431		RealType c1, c2, c3, c4;
432	<	RealType erfcVal, derfcVal;
432	>	RealType erfcVal(1.0), derfcVal(0.0);
433		RealType BigR;
434	+	RealType two(2.0), three(3.0);
435
436		Vector3d Q_i, Q_j;
437		Vector3d ux_i, uy_i, uz_i;
#	Line 367 \| Line 441 \| namespace OpenMD {
441		Vector3d rhatdot2, rhatc4;
442		Vector3d dVdr;
443
444	+	// variables for indirect (reaction field) interactions for excluded pairs:
445	+	RealType indirect_Pot(0.0);
446	+	RealType indirect_vpair(0.0);
447	+	Vector3d indirect_dVdr(V3Zero);
448	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
449	+
450	+	RealType coulInt, vFluc1(0.0), vFluc2(0.0);
451		pair<RealType, RealType> res;
452
453	+	// splines for coulomb integrals
454	+	CubicSpline* J1;
455	+	CubicSpline* J2;
456	+
457		if (!initialized_) initialize();
458
459	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
460	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
459	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
460	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
461
462		// some variables we'll need independent of electrostatic type:
463
464	<	riji = 1.0 / idat.rij;
465	<	Vector3d rhat = idat.d * riji;
464	>	riji = 1.0 / *(idat.rij) ;
465	>	Vector3d rhat = (idat.d) riji;
466
467		// logicals
468
#	Line 385 \| Line 470 \| namespace OpenMD {
470		bool i_is_Dipole = data1.is_Dipole;
471		bool i_is_SplitDipole = data1.is_SplitDipole;
472		bool i_is_Quadrupole = data1.is_Quadrupole;
473	+	bool i_is_Fluctuating = data1.is_Fluctuating;
474
475		bool j_is_Charge = data2.is_Charge;
476		bool j_is_Dipole = data2.is_Dipole;
477		bool j_is_SplitDipole = data2.is_SplitDipole;
478		bool j_is_Quadrupole = data2.is_Quadrupole;
479	+	bool j_is_Fluctuating = data2.is_Fluctuating;
480
481	<	if (i_is_Charge)
482	<	q_i = data1.charge;
481	>	if (i_is_Charge) {
482	>	q_i = data1.fixedCharge;
483
484	+	if (i_is_Fluctuating) {
485	+	q_i += *(idat.flucQ1);
486	+	}
487	+
488	+	if (idat.excluded) {
489	+	*(idat.skippedCharge2) += q_i;
490	+	}
491	+	}
492	+
493		if (i_is_Dipole) {
494		mu_i = data1.dipole_moment;
495	<	uz_i = idat.eFrame1.getColumn(2);
495	>	uz_i = idat.eFrame1->getColumn(2);
496
497		ct_i = dot(uz_i, rhat);
498
#	Line 412 \| Line 508 \| namespace OpenMD {
508		qyy_i = Q_i.y();
509		qzz_i = Q_i.z();
510
511	<	ux_i = idat.eFrame1.getColumn(0);
512	<	uy_i = idat.eFrame1.getColumn(1);
513	<	uz_i = idat.eFrame1.getColumn(2);
511	>	ux_i = idat.eFrame1->getColumn(0);
512	>	uy_i = idat.eFrame1->getColumn(1);
513	>	uz_i = idat.eFrame1->getColumn(2);
514
515		cx_i = dot(ux_i, rhat);
516		cy_i = dot(uy_i, rhat);
#	Line 425 \| Line 521 \| namespace OpenMD {
521		duduz_i = V3Zero;
522		}
523
524	<	if (j_is_Charge)
525	<	q_j = data2.charge;
524	>	if (j_is_Charge) {
525	>	q_j = data2.fixedCharge;
526
527	+	if (i_is_Fluctuating)
528	+	q_j += *(idat.flucQ2);
529	+
530	+	if (idat.excluded) {
531	+	*(idat.skippedCharge1) += q_j;
532	+	}
533	+	}
534	+
535	+
536		if (j_is_Dipole) {
537		mu_j = data2.dipole_moment;
538	<	uz_j = idat.eFrame2.getColumn(2);
538	>	uz_j = idat.eFrame2->getColumn(2);
539
540		ct_j = dot(uz_j, rhat);
541
#	Line 446 \| Line 551 \| namespace OpenMD {
551		qyy_j = Q_j.y();
552		qzz_j = Q_j.z();
553
554	<	ux_j = idat.eFrame2.getColumn(0);
555	<	uy_j = idat.eFrame2.getColumn(1);
556	<	uz_j = idat.eFrame2.getColumn(2);
554	>	ux_j = idat.eFrame2->getColumn(0);
555	>	uy_j = idat.eFrame2->getColumn(1);
556	>	uz_j = idat.eFrame2->getColumn(2);
557
558		cx_j = dot(ux_j, rhat);
559		cy_j = dot(uy_j, rhat);
#	Line 459 \| Line 564 \| namespace OpenMD {
564		duduz_j = V3Zero;
565		}
566
567	+	if (i_is_Fluctuating && j_is_Fluctuating) {
568	+	J1 = Jij[idat.atypes];
569	+	J2 = Jij[make_pair(idat.atypes.second, idat.atypes.first)];
570	+	}
571	+
572		epot = 0.0;
573		dVdr = V3Zero;
574
#	Line 467 \| Line 577 \| namespace OpenMD {
577		if (j_is_Charge) {
578		if (screeningMethod_ == DAMPED) {
579		// assemble the damping variables
580	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
581	<	erfcVal = res.first;
582	<	derfcVal = res.second;
580	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
581	>	//erfcVal = res.first;
582	>	//derfcVal = res.second;
583	>
584	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
585	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
586	>
587		c1 = erfcVal * riji;
588		c2 = (-derfcVal + c1) * riji;
589		} else {
#	Line 477 \| Line 591 \| namespace OpenMD {
591		c2 = c1 * riji;
592		}
593
594	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
594	>	preVal = (idat.electroMult) pre11_ * q_i * q_j;
595
596	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
596	>	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
597		vterm = preVal * (c1 - c1c_);
598	<	dudr = -idat.sw * preVal * c2;
485	<
486	<	} else if (summationMethod_ == SHIFTED_FORCE) {
487	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
488	<	dudr = idat.sw * preVal * (c2c_ - c2);
489	<
490	<	} else if (summationMethod_ == REACTION_FIELD) {
491	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
492	<	vterm = preVal * ( riji + rfVal );
493	<	dudr = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
598	>	dudr = - (idat.sw) preVal * c2;
599
600	+	} else if (summationMethod_ == esm_SHIFTED_FORCE) {
601	+	vterm = preVal * ( c1 - c1c_ + c2c_( (idat.rij) - cutoffRadius_) );
602	+	dudr = (idat.sw) preVal * (c2c_ - c2);
603	+
604	+	} else if (summationMethod_ == esm_REACTION_FIELD) {
605	+	rfVal = preRF_ * (idat.rij) *(idat.rij);
606	+
607	+	vterm = preVal * ( riji + rfVal );
608	+	dudr = (idat.sw) preVal * ( 2.0 * rfVal - riji ) * riji;
609	+
610	+	// if this is an excluded pair, there are still indirect
611	+	// interactions via the reaction field we must worry about:
612	+
613	+	if (idat.excluded) {
614	+	indirect_vpair += preVal * rfVal;
615	+	indirect_Pot += (idat.sw) preVal * rfVal;
616	+	indirect_dVdr += (idat.sw) preVal * two * rfVal * riji * rhat;
617	+	}
618	+
619		} else {
496	–	vterm = preVal * riji * erfcVal;
620
621	<	dudr = - idat.sw * preVal * c2;
621	>	vterm = preVal * riji * erfcVal;
622	>	dudr = - (idat.sw) preVal * c2;
623	>
624	>	}
625	>
626	>	vpair += vterm;
627	>	epot += (idat.sw) vterm;
628	>	dVdr += dudr * rhat;
629
630	+	if (i_is_Fluctuating) {
631	+	if (idat.excluded) {
632	+	// vFluc1 is the difference between the direct coulomb integral
633	+	// and the normal 1/r-like interaction between point charges.
634	+	coulInt = J1->getValueAt( *(idat.rij) );
635	+	vFluc1 = pre11_ * coulInt * q_i * q_j - ((idat.sw) vterm);
636	+	} else {
637	+	vFluc1 = 0.0;
638	+	}
639	+	(idat.dVdFQ1) += ( (idat.sw) * vterm + vFluc1 ) / q_i;
640		}
501	–
502	–	idat.vpair += vterm;
503	–	epot += idat.sw * vterm;
641
642	<	dVdr += dudr * rhat;
642	>	if (j_is_Fluctuating) {
643	>	if (idat.excluded) {
644	>	// vFluc2 is the difference between the direct coulomb integral
645	>	// and the normal 1/r-like interaction between point charges.
646	>	coulInt = J2->getValueAt( *(idat.rij) );
647	>	vFluc2 = pre11_ * coulInt * q_i * q_j - ((idat.sw) vterm);
648	>	} else {
649	>	vFluc2 = 0.0;
650	>	}
651	>	(idat.dVdFQ2) += ( (idat.sw) * vterm + vFluc2 ) / q_j;
652	>	}
653	>
654	>
655		}
656
657		if (j_is_Dipole) {
658		// pref is used by all the possible methods
659	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
660	<	preSw = idat.sw * pref;
659	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
660	>	preSw = (idat.sw) pref;
661
662	<	if (summationMethod_ == REACTION_FIELD) {
662	>	if (summationMethod_ == esm_REACTION_FIELD) {
663		ri2 = riji * riji;
664		ri3 = ri2 * riji;
665
666	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
667	<	idat.vpair += vterm;
668	<	epot += idat.sw * vterm;
666	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
667	>	vpair += vterm;
668	>	epot += (idat.sw) vterm;
669
670	<	dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
671	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
670	>	dVdr += -preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
671	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
672
673	+	// Even if we excluded this pair from direct interactions,
674	+	// we still have the reaction-field-mediated charge-dipole
675	+	// interaction:
676	+
677	+	if (idat.excluded) {
678	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
679	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
680	+	indirect_dVdr += preSw * preRF2_ * uz_j;
681	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
682	+	}
683	+
684		} else {
685		// determine the inverse r used if we have split dipoles
686		if (j_is_SplitDipole) {
687	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
687	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
688		ri = 1.0 / BigR;
689	<	scale = idat.rij * ri;
689	>	scale = (idat.rij) ri;
690		} else {
691		ri = riji;
692		scale = 1.0;
#	Line 536 \| Line 696 \| namespace OpenMD {
696
697		if (screeningMethod_ == DAMPED) {
698		// assemble the damping variables
699	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
700	<	erfcVal = res.first;
701	<	derfcVal = res.second;
699	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
700	>	//erfcVal = res.first;
701	>	//derfcVal = res.second;
702	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
703	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
704		c1 = erfcVal * ri;
705		c2 = (-derfcVal + c1) * ri;
706		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 553 \| Line 715 \| namespace OpenMD {
715		// calculate the potential
716		pot_term = scale * c2;
717		vterm = -pref * ct_j * pot_term;
718	<	idat.vpair += vterm;
719	<	epot += idat.sw * vterm;
718	>	vpair += vterm;
719	>	epot += (idat.sw) vterm;
720
721		// calculate derivatives for forces and torques
722
#	Line 562 \| Line 724 \| namespace OpenMD {
724		duduz_j += -preSw * pot_term * rhat;
725
726		}
727	+	if (i_is_Fluctuating) {
728	+	(idat.dVdFQ1) += ( (idat.sw) * vterm ) / q_i;
729	+	}
730		}
731
732		if (j_is_Quadrupole) {
#	Line 569 \| Line 734 \| namespace OpenMD {
734		cx2 = cx_j * cx_j;
735		cy2 = cy_j * cy_j;
736		cz2 = cz_j * cz_j;
737	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
737	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
738
739		if (screeningMethod_ == DAMPED) {
740		// assemble the damping variables
741	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
742	<	erfcVal = res.first;
743	<	derfcVal = res.second;
741	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
742	>	//erfcVal = res.first;
743	>	//derfcVal = res.second;
744	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
745	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
746		c1 = erfcVal * riji;
747		c2 = (-derfcVal + c1) * riji;
748		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 588 \| Line 755 \| namespace OpenMD {
755		}
756
757		// precompute variables for convenience
758	<	preSw = idat.sw * pref;
758	>	preSw = (idat.sw) pref;
759		c2ri = c2 * riji;
760		c3ri = c3 * riji;
761	<	c4rij = c4 * idat.rij;
762	<	rhatdot2 = 2.0 * rhat * c3;
761	>	c4rij = c4 * *(idat.rij) ;
762	>	rhatdot2 = two * rhat * c3;
763		rhatc4 = rhat * c4rij;
764
765		// calculate the potential
#	Line 600 \| Line 767 \| namespace OpenMD {
767		qyy_j * (cy2*c3 - c2ri) +
768		qzz_j * (cz2*c3 - c2ri) );
769		vterm = pref * pot_term;
770	<	idat.vpair += vterm;
771	<	epot += idat.sw * vterm;
770	>	vpair += vterm;
771	>	epot += (idat.sw) vterm;
772
773		// calculate derivatives for the forces and torques
774
775	<	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (2.0cx_jux_j + rhat)c3ri) +
776	<	qyy_j* (cy2rhatc4 - (2.0cy_juy_j + rhat)c3ri) +
777	<	qzz_j* (cz2rhatc4 - (2.0cz_juz_j + rhat)c3ri));
775	>	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (twocx_jux_j + rhat)c3ri) +
776	>	qyy_j* (cy2rhatc4 - (twocy_juy_j + rhat)c3ri) +
777	>	qzz_j* (cz2rhatc4 - (twocz_juz_j + rhat)c3ri));
778
779		dudux_j += preSw * qxx_j * cx_j * rhatdot2;
780		duduy_j += preSw * qyy_j * cy_j * rhatdot2;
781		duduz_j += preSw * qzz_j * cz_j * rhatdot2;
782	+	if (i_is_Fluctuating) {
783	+	(idat.dVdFQ1) += ( (idat.sw) * vterm ) / q_i;
784	+	}
785	+
786		}
787		}
788
#	Line 619 \| Line 790 \| namespace OpenMD {
790
791		if (j_is_Charge) {
792		// variables used by all the methods
793	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
794	<	preSw = idat.sw * pref;
793	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
794	>	preSw = (idat.sw) pref;
795
796	<	if (summationMethod_ == REACTION_FIELD) {
796	>	if (summationMethod_ == esm_REACTION_FIELD) {
797
798		ri2 = riji * riji;
799		ri3 = ri2 * riji;
800
801	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
802	<	idat.vpair += vterm;
803	<	epot += idat.sw * vterm;
801	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
802	>	vpair += vterm;
803	>	epot += (idat.sw) vterm;
804
805	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
805	>	dVdr += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_ * uz_i);
806
807	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
807	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
808	>
809	>	// Even if we excluded this pair from direct interactions,
810	>	// we still have the reaction-field-mediated charge-dipole
811	>	// interaction:
812	>
813	>	if (idat.excluded) {
814	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
815	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
816	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
817	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
818	>	}
819
820		} else {
821
822		// determine inverse r if we are using split dipoles
823		if (i_is_SplitDipole) {
824	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
824	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
825		ri = 1.0 / BigR;
826	<	scale = idat.rij * ri;
826	>	scale = (idat.rij) ri;
827		} else {
828		ri = riji;
829		scale = 1.0;
#	Line 651 \| Line 833 \| namespace OpenMD {
833
834		if (screeningMethod_ == DAMPED) {
835		// assemble the damping variables
836	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
837	<	erfcVal = res.first;
838	<	derfcVal = res.second;
836	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
837	>	//erfcVal = res.first;
838	>	//derfcVal = res.second;
839	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
840	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
841		c1 = erfcVal * ri;
842		c2 = (-derfcVal + c1) * ri;
843		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 668 \| Line 852 \| namespace OpenMD {
852		// calculate the potential
853		pot_term = c2 * scale;
854		vterm = pref * ct_i * pot_term;
855	<	idat.vpair += vterm;
856	<	epot += idat.sw * vterm;
855	>	vpair += vterm;
856	>	epot += (idat.sw) vterm;
857
858		// calculate derivatives for the forces and torques
859		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
860		duduz_i += preSw * pot_term * rhat;
861		}
862	+
863	+	if (j_is_Fluctuating) {
864	+	(idat.dVdFQ2) += ( (idat.sw) * vterm ) / q_j;
865	+	}
866	+
867		}
868
869		if (j_is_Dipole) {
870		// variables used by all methods
871		ct_ij = dot(uz_i, uz_j);
872
873	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
874	<	preSw = idat.sw * pref;
873	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
874	>	preSw = (idat.sw) pref;
875
876	<	if (summationMethod_ == REACTION_FIELD) {
876	>	if (summationMethod_ == esm_REACTION_FIELD) {
877		ri2 = riji * riji;
878		ri3 = ri2 * riji;
879		ri4 = ri2 * ri2;
880
881		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
882		preRF2_ * ct_ij );
883	<	idat.vpair += vterm;
884	<	epot += idat.sw * vterm;
883	>	vpair += vterm;
884	>	epot += (idat.sw) vterm;
885
886		a1 = 5.0 * ct_i * ct_j - ct_ij;
887
888	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
888	>	dVdr += preSw * three * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
889
890	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
891	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
890	>	duduz_i += preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
891	>	duduz_j += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_*uz_i);
892
893	+	if (idat.excluded) {
894	+	indirect_vpair += - pref * preRF2_ * ct_ij;
895	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
896	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
897	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
898	+	}
899	+
900		} else {
901
902		if (i_is_SplitDipole) {
903		if (j_is_SplitDipole) {
904	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
904	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
905		} else {
906	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
906	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
907		}
908		ri = 1.0 / BigR;
909	<	scale = idat.rij * ri;
909	>	scale = (idat.rij) ri;
910		} else {
911		if (j_is_SplitDipole) {
912	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
912	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
913		ri = 1.0 / BigR;
914	<	scale = idat.rij * ri;
914	>	scale = (idat.rij) ri;
915		} else {
916		ri = riji;
917		scale = 1.0;
#	Line 723 \| Line 919 \| namespace OpenMD {
919		}
920		if (screeningMethod_ == DAMPED) {
921		// assemble damping variables
922	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
923	<	erfcVal = res.first;
924	<	derfcVal = res.second;
922	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
923	>	//erfcVal = res.first;
924	>	//derfcVal = res.second;
925	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
926	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
927		c1 = erfcVal * ri;
928		c2 = (-derfcVal + c1) * ri;
929		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 745 \| Line 943 \| namespace OpenMD {
943		preSwSc = preSw * scale;
944		c2ri = c2 * ri;
945		c3ri = c3 * ri;
946	<	c4rij = c4 * idat.rij;
946	>	c4rij = c4 * *(idat.rij) ;
947
948		// calculate the potential
949		pot_term = (ct_ij * c2ri - ctidotj * c3);
950		vterm = pref * pot_term;
951	<	idat.vpair += vterm;
952	<	epot += idat.sw * vterm;
951	>	vpair += vterm;
952	>	epot += (idat.sw) vterm;
953
954		// calculate derivatives for the forces and torques
955		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 770 \| Line 968 \| namespace OpenMD {
968		cy2 = cy_i * cy_i;
969		cz2 = cz_i * cz_i;
970
971	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
971	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
972
973		if (screeningMethod_ == DAMPED) {
974		// assemble the damping variables
975	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
976	<	erfcVal = res.first;
977	<	derfcVal = res.second;
975	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
976	>	//erfcVal = res.first;
977	>	//derfcVal = res.second;
978	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
979	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
980		c1 = erfcVal * riji;
981		c2 = (-derfcVal + c1) * riji;
982		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 789 \| Line 989 \| namespace OpenMD {
989		}
990
991		// precompute some variables for convenience
992	<	preSw = idat.sw * pref;
992	>	preSw = (idat.sw) pref;
993		c2ri = c2 * riji;
994		c3ri = c3 * riji;
995	<	c4rij = c4 * idat.rij;
996	<	rhatdot2 = 2.0 * rhat * c3;
995	>	c4rij = c4 * *(idat.rij) ;
996	>	rhatdot2 = two * rhat * c3;
997		rhatc4 = rhat * c4rij;
998
999		// calculate the potential
#	Line 802 \| Line 1002 \| namespace OpenMD {
1002		qzz_i * (cz2 * c3 - c2ri) );
1003
1004		vterm = pref * pot_term;
1005	<	idat.vpair += vterm;
1006	<	epot += idat.sw * vterm;
1005	>	vpair += vterm;
1006	>	epot += (idat.sw) vterm;
1007
1008		// calculate the derivatives for the forces and torques
1009
1010	<	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (2.0cx_iux_i + rhat)c3ri) +
1011	<	qyy_i* (cy2rhatc4 - (2.0cy_iuy_i + rhat)c3ri) +
1012	<	qzz_i* (cz2rhatc4 - (2.0cz_iuz_i + rhat)c3ri));
1010	>	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (twocx_iux_i + rhat)c3ri) +
1011	>	qyy_i* (cy2rhatc4 - (twocy_iuy_i + rhat)c3ri) +
1012	>	qzz_i* (cz2rhatc4 - (twocz_iuz_i + rhat)c3ri));
1013
1014		dudux_i += preSw * qxx_i * cx_i * rhatdot2;
1015		duduy_i += preSw * qyy_i * cy_i * rhatdot2;
1016		duduz_i += preSw * qzz_i * cz_i * rhatdot2;
817	–	}
818	–	}
1017
1018	<	idat.pot += epot;
1019	<	idat.f1 += dVdr;
1018	>	if (j_is_Fluctuating) {
1019	>	(idat.dVdFQ2) += ( (idat.sw) * vterm ) / q_j;
1020	>	}
1021
1022	<	if (i_is_Dipole \|\| i_is_Quadrupole)
824	<	idat.t1 -= cross(uz_i, duduz_i);
825	<	if (i_is_Quadrupole) {
826	<	idat.t1 -= cross(ux_i, dudux_i);
827	<	idat.t1 -= cross(uy_i, duduy_i);
1022	>	}
1023		}
1024
830	–	if (j_is_Dipole \|\| j_is_Quadrupole)
831	–	idat.t2 -= cross(uz_j, duduz_j);
832	–	if (j_is_Quadrupole) {
833	–	idat.t2 -= cross(uz_j, dudux_j);
834	–	idat.t2 -= cross(uz_j, duduy_j);
835	–	}
1025
1026	<	return;
1027	<	}
1026	>	if (!idat.excluded) {
1027	>	*(idat.vpair) += vpair;
1028	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
1029	>	*(idat.f1) += dVdr;
1030	>
1031	>	if (i_is_Dipole \|\| i_is_Quadrupole)
1032	>	*(idat.t1) -= cross(uz_i, duduz_i);
1033	>	if (i_is_Quadrupole) {
1034	>	*(idat.t1) -= cross(ux_i, dudux_i);
1035	>	*(idat.t1) -= cross(uy_i, duduy_i);
1036	>	}
1037	>
1038	>	if (j_is_Dipole \|\| j_is_Quadrupole)
1039	>	*(idat.t2) -= cross(uz_j, duduz_j);
1040	>	if (j_is_Quadrupole) {
1041	>	*(idat.t2) -= cross(uz_j, dudux_j);
1042	>	*(idat.t2) -= cross(uz_j, duduy_j);
1043	>	}
1044
1045	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
1045	>	} else {
1046
1047	<	if (!initialized_) initialize();
1048	<
844	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
845	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
846	<
847	<	// logicals
1047	>	// only accumulate the forces and torques resulting from the
1048	>	// indirect reaction field terms.
1049
1050	<	bool i_is_Charge = data1.is_Charge;
1051	<	bool i_is_Dipole = data1.is_Dipole;
1052	<
852	<	bool j_is_Charge = data2.is_Charge;
853	<	bool j_is_Dipole = data2.is_Dipole;
854	<
855	<	RealType q_i, q_j;
856	<
857	<	// The skippedCharge computation is needed by the real-space cutoff methods
858	<	// (i.e. shifted force and shifted potential)
859	<
860	<	if (i_is_Charge) {
861	<	q_i = data1.charge;
862	<	skdat.skippedCharge2 += q_i;
863	<	}
864	<
865	<	if (j_is_Charge) {
866	<	q_j = data2.charge;
867	<	skdat.skippedCharge1 += q_j;
868	<	}
869	<
870	<	// the rest of this function should only be necessary for reaction field.
871	<
872	<	if (summationMethod_ == REACTION_FIELD) {
873	<	RealType riji, ri2, ri3;
874	<	RealType q_i, mu_i, ct_i;
875	<	RealType q_j, mu_j, ct_j;
876	<	RealType preVal, rfVal, vterm, dudr, pref, myPot;
877	<	Vector3d dVdr, uz_i, uz_j, duduz_i, duduz_j, rhat;
878	<
879	<	// some variables we'll need independent of electrostatic type:
1050	>	*(idat.vpair) += indirect_vpair;
1051	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
1052	>	*(idat.f1) += indirect_dVdr;
1053
881	–	riji = 1.0 / skdat.rij;
882	–	rhat = skdat.d * riji;
883	–
884	–	if (i_is_Dipole) {
885	–	mu_i = data1.dipole_moment;
886	–	uz_i = skdat.eFrame1.getColumn(2);
887	–	ct_i = dot(uz_i, rhat);
888	–	duduz_i = V3Zero;
889	–	}
890	–
891	–	if (j_is_Dipole) {
892	–	mu_j = data2.dipole_moment;
893	–	uz_j = skdat.eFrame2.getColumn(2);
894	–	ct_j = dot(uz_j, rhat);
895	–	duduz_j = V3Zero;
896	–	}
897	–
898	–	if (i_is_Charge) {
899	–	if (j_is_Charge) {
900	–	preVal = skdat.electroMult * pre11_ * q_i * q_j;
901	–	rfVal = preRF_ * skdat.rij * skdat.rij;
902	–	vterm = preVal * rfVal;
903	–	myPot += skdat.sw * vterm;
904	–	dudr = skdat.sw * preVal * 2.0 * rfVal * riji;
905	–	dVdr += dudr * rhat;
906	–	}
907	–
908	–	if (j_is_Dipole) {
909	–	ri2 = riji * riji;
910	–	ri3 = ri2 * riji;
911	–	pref = skdat.electroMult * pre12_ * q_i * mu_j;
912	–	vterm = - pref * ct_j * ( ri2 - preRF2_ * skdat.rij );
913	–	myPot += skdat.sw * vterm;
914	–	dVdr += -skdat.sw * pref * ( ri3 * ( uz_j - 3.0 * ct_j * rhat) - preRF2_ * uz_j);
915	–	duduz_j += -skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
916	–	}
917	–	}
918	–	if (i_is_Dipole) {
919	–	if (j_is_Charge) {
920	–	ri2 = riji * riji;
921	–	ri3 = ri2 * riji;
922	–	pref = skdat.electroMult * pre12_ * q_j * mu_i;
923	–	vterm = - pref * ct_i * ( ri2 - preRF2_ * skdat.rij );
924	–	myPot += skdat.sw * vterm;
925	–	dVdr += skdat.sw * pref * ( ri3 * ( uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
926	–	duduz_i += skdat.sw * pref * rhat * (ri2 - preRF2_ * skdat.rij);
927	–	}
928	–	}
929	–
930	–	// accumulate the forces and torques resulting from the self term
931	–	skdat.pot += myPot;
932	–	skdat.f1 += dVdr;
933	–
1054		if (i_is_Dipole)
1055	<	skdat.t1 -= cross(uz_i, duduz_i);
1055	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
1056		if (j_is_Dipole)
1057	<	skdat.t2 -= cross(uz_j, duduz_j);
1057	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
1058		}
1059	<	}
1059	>
1060	>	return;
1061	>	}
1062
1063	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1063	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1064		RealType mu1, preVal, chg1, self;
1065
1066		if (!initialized_) initialize();
1067	<
1068	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1067	>
1068	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1069
1070		// logicals
949	–
1071		bool i_is_Charge = data.is_Charge;
1072		bool i_is_Dipole = data.is_Dipole;
1073
1074	<	if (summationMethod_ == REACTION_FIELD) {
1074	>	if (summationMethod_ == esm_REACTION_FIELD) {
1075		if (i_is_Dipole) {
1076		mu1 = data.dipole_moment;
1077		preVal = pre22_ * preRF2_ * mu1 * mu1;
1078	<	scdat.pot -= 0.5 * preVal;
1078	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1079
1080		// The self-correction term adds into the reaction field vector
1081	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1081	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1082		Vector3d ei = preVal * uz_i;
1083
1084		// This looks very wrong. A vector crossed with itself is zero.
1085	<	scdat.t -= cross(uz_i, ei);
1085	>	*(sdat.t) -= cross(uz_i, ei);
1086		}
1087	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1087	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1088		if (i_is_Charge) {
1089	<	chg1 = data.charge;
1089	>	chg1 = data.fixedCharge;
1090		if (screeningMethod_ == DAMPED) {
1091	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1091	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1092		} else {
1093	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1093	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1094		}
1095	<	scdat.pot += self;
1095	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1096		}
1097		}
1098		}
1099	+
1100	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1101	+	// This seems to work moderately well as a default. There's no
1102	+	// inherent scale for 1/r interactions that we can standardize.
1103	+	// 12 angstroms seems to be a reasonably good guess for most
1104	+	// cases.
1105	+	return 12.0;
1106	+	}
1107		}

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Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents): Revision 1504 by gezelter, Sat Oct 2 20:41:53 2010 UTC vs. Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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Comparing branches/development/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1504 by gezelter, Sat Oct 2 20:41:53 2010 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC