[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 1750 by gezelter, Thu Jun 7 12:53:46 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\n"
197	+	"\tinput file. A default value of %f (1/ang) will be used for the\n"
198	+	"\tcutoff of %f (ang).\n",
199	+	dampingAlpha_, cutoffRadius_);
200	+	painCave.severity = OPENMD_INFO;
201	+	painCave.isFatal = 0;
202	+	simError();
203	+	} else {
204	+	dampingAlpha_ = simParams_->getDampingAlpha();
205	+	}
206	+	haveDampingAlpha_ = true;
207	+	}
208	+
209		// find all of the Electrostatic atom Types:
210		ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
211		ForceField::AtomTypeContainer::MapTypeIterator i;
212		AtomType* at;
213	<
213	>
214		for (at = atomTypes->beginType(i); at != NULL;
215		at = atomTypes->nextType(i)) {
216
#	Line 100 \| Line 218 \| namespace OpenMD {
218		addType(at);
219		}
220
221	<	// check to make sure a cutoff value has been set:
222	<	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_;
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 185 \| Line 284 \| namespace OpenMD {
284		electrostaticAtomData.is_Dipole = false;
285		electrostaticAtomData.is_SplitDipole = false;
286		electrostaticAtomData.is_Quadrupole = false;
287	+	electrostaticAtomData.is_Fluctuating = false;
288
289	<	if (atomType->isCharge()) {
190	<	GenericData* data = atomType->getPropertyByName("Charge");
289	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
290
291	<	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	<	}
291	>	if (fca.isFixedCharge()) {
292		electrostaticAtomData.is_Charge = true;
293	<	electrostaticAtomData.charge = doubleData->getData();
293	>	electrostaticAtomData.fixedCharge = fca.getCharge();
294		}
295
296	<	if (atomType->isDirectional()) {
297	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
298	<
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	<	}
296	>	MultipoleAdapter ma = MultipoleAdapter(atomType);
297	>	if (ma.isMultipole()) {
298	>	if (ma.isDipole()) {
299		electrostaticAtomData.is_Dipole = true;
300	<	electrostaticAtomData.dipole_moment = doubleData->getData();
300	>	electrostaticAtomData.dipole_moment = ma.getDipoleMoment();
301		}
302	<
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	<	}
302	>	if (ma.isSplitDipole()) {
303		electrostaticAtomData.is_SplitDipole = true;
304	<	electrostaticAtomData.split_dipole_distance = doubleData->getData();
304	>	electrostaticAtomData.split_dipole_distance = ma.getSplitDipoleDistance();
305		}
306	<
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	<
306	>	if (ma.isQuadrupole()) {
307		// Quadrupoles in OpenMD are set as the diagonal elements
308		// of the diagonalized traceless quadrupole moment tensor.
309		// The column vectors of the unitary matrix that diagonalizes
310		// the quadrupole moment tensor become the eFrame (or the
311		// 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	–	}
312		electrostaticAtomData.is_Quadrupole = true;
313	<	electrostaticAtomData.quadrupole_moments = v3dData->getData();
313	>	electrostaticAtomData.quadrupole_moments = ma.getQuadrupoleMoments();
314		}
315		}
316
317	<	AtomTypeProperties atp = atomType->getATP();
317	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
318
319	+	if (fqa.isFluctuatingCharge()) {
320	+	electrostaticAtomData.is_Fluctuating = true;
321	+	electrostaticAtomData.electronegativity = fqa.getElectronegativity();
322	+	electrostaticAtomData.hardness = fqa.getHardness();
323	+	electrostaticAtomData.slaterN = fqa.getSlaterN();
324	+	electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
325	+	}
326	+
327		pair<map<int,AtomType*>::iterator,bool> ret;
328	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
328	>	ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
329	>	atomType) );
330		if (ret.second == false) {
331		sprintf( painCave.errMsg,
332		"Electrostatic already had a previous entry with ident %d\n",
333	<	atp.ident);
333	>	atomType->getIdent() );
334		painCave.severity = OPENMD_INFO;
335		painCave.isFatal = 0;
336		simError();
337		}
338
339	<	ElectrostaticMap[atomType] = electrostaticAtomData;
339	>	ElectrostaticMap[atomType] = electrostaticAtomData;
340	>
341	>	// Now, iterate over all known types and add to the mixing map:
342	>
343	>	map<AtomType*, ElectrostaticAtomData>::iterator it;
344	>	for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
345	>	AtomType* atype2 = (*it).first;
346	>	ElectrostaticAtomData eaData2 = (*it).second;
347	>	if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) {
348	>
349	>	RealType a = electrostaticAtomData.slaterZeta;
350	>	RealType b = eaData2.slaterZeta;
351	>	int m = electrostaticAtomData.slaterN;
352	>	int n = eaData2.slaterN;
353	>
354	>	// Create the spline of the coulombic integral for s-type
355	>	// Slater orbitals. Add a 2 angstrom safety window to deal
356	>	// with cutoffGroups that have charged atoms longer than the
357	>	// cutoffRadius away from each other.
358	>
359	>	RealType rval;
360	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
361	>	vector<RealType> rvals;
362	>	vector<RealType> J1vals;
363	>	vector<RealType> J2vals;
364	>	for (int i = 0; i < np_; i++) {
365	>	rval = RealType(i) * dr;
366	>	rvals.push_back(rval);
367	>	J1vals.push_back(electrostaticAtomData.hardness * sSTOCoulInt( a, b, m, n, rval * PhysicalConstants::angstromsToBohr ) );
368	>	// may not be necessary if Slater coulomb integral is symmetric
369	>	J2vals.push_back(eaData2.hardness * sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) );
370	>	}
371	>
372	>	CubicSpline* J1 = new CubicSpline();
373	>	J1->addPoints(rvals, J1vals);
374	>	CubicSpline* J2 = new CubicSpline();
375	>	J2->addPoints(rvals, J2vals);
376	>
377	>	pair<AtomType, AtomType> key1, key2;
378	>	key1 = make_pair(atomType, atype2);
379	>	key2 = make_pair(atype2, atomType);
380	>
381	>	Jij[key1] = J1;
382	>	Jij[key2] = J2;
383	>	}
384	>	}
385	>
386		return;
387		}
388
389	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
390	<	RealType theRSW ) {
391	<	defaultCutoff_ = theECR;
392	<	rrf_ = defaultCutoff_;
328	<	rt_ = theRSW;
329	<	haveDefaultCutoff_ = true;
389	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
390	>	cutoffRadius_ = rCut;
391	>	rrf_ = cutoffRadius_;
392	>	haveCutoffRadius_ = true;
393		}
394	+
395	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
396	+	rt_ = rSwitch;
397	+	}
398		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
399		summationMethod_ = esm;
400		}
#	Line 343 \| Line 410 \| namespace OpenMD {
410		haveDielectric_ = true;
411		}
412
413	<	void Electrostatic::calcForce(InteractionData idat) {
413	>	void Electrostatic::calcForce(InteractionData &idat) {
414
415		// utility variables. Should clean these up and use the Vector3d and
416		// Mat3x3d to replace as many as we can in future versions:
#	Line 357 \| Line 424 \| namespace OpenMD {
424		RealType ct_i, ct_j, ct_ij, a1;
425		RealType riji, ri, ri2, ri3, ri4;
426		RealType pref, vterm, epot, dudr;
427	+	RealType vpair(0.0);
428		RealType scale, sc2;
429		RealType pot_term, preVal, rfVal;
430		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
431		RealType preSw, preSwSc;
432		RealType c1, c2, c3, c4;
433	<	RealType erfcVal, derfcVal;
433	>	RealType erfcVal(1.0), derfcVal(0.0);
434		RealType BigR;
435	+	RealType two(2.0), three(3.0);
436
437		Vector3d Q_i, Q_j;
438		Vector3d ux_i, uy_i, uz_i;
#	Line 373 \| Line 442 \| namespace OpenMD {
442		Vector3d rhatdot2, rhatc4;
443		Vector3d dVdr;
444
445	+	// variables for indirect (reaction field) interactions for excluded pairs:
446	+	RealType indirect_Pot(0.0);
447	+	RealType indirect_vpair(0.0);
448	+	Vector3d indirect_dVdr(V3Zero);
449	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
450	+
451	+	RealType coulInt, vFluc1(0.0), vFluc2(0.0);
452		pair<RealType, RealType> res;
453
454	+	// splines for coulomb integrals
455	+	CubicSpline* J1;
456	+	CubicSpline* J2;
457	+
458		if (!initialized_) initialize();
459
460	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
461	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
460	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
461	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
462
463		// some variables we'll need independent of electrostatic type:
464
465	<	riji = 1.0 / idat.rij;
466	<	Vector3d rhat = idat.d * riji;
465	>	riji = 1.0 / *(idat.rij) ;
466	>	Vector3d rhat = (idat.d) riji;
467
468		// logicals
469
#	Line 391 \| Line 471 \| namespace OpenMD {
471		bool i_is_Dipole = data1.is_Dipole;
472		bool i_is_SplitDipole = data1.is_SplitDipole;
473		bool i_is_Quadrupole = data1.is_Quadrupole;
474	+	bool i_is_Fluctuating = data1.is_Fluctuating;
475
476		bool j_is_Charge = data2.is_Charge;
477		bool j_is_Dipole = data2.is_Dipole;
478		bool j_is_SplitDipole = data2.is_SplitDipole;
479		bool j_is_Quadrupole = data2.is_Quadrupole;
480	+	bool j_is_Fluctuating = data2.is_Fluctuating;
481
482	<	if (i_is_Charge)
483	<	q_i = data1.charge;
482	>	if (i_is_Charge) {
483	>	q_i = data1.fixedCharge;
484
485	+	if (i_is_Fluctuating) {
486	+	q_i += *(idat.flucQ1);
487	+	}
488	+
489	+	if (idat.excluded) {
490	+	*(idat.skippedCharge2) += q_i;
491	+	}
492	+	}
493	+
494		if (i_is_Dipole) {
495		mu_i = data1.dipole_moment;
496	<	uz_i = idat.eFrame1.getColumn(2);
496	>	uz_i = idat.eFrame1->getColumn(2);
497
498		ct_i = dot(uz_i, rhat);
499
#	Line 418 \| Line 509 \| namespace OpenMD {
509		qyy_i = Q_i.y();
510		qzz_i = Q_i.z();
511
512	<	ux_i = idat.eFrame1.getColumn(0);
513	<	uy_i = idat.eFrame1.getColumn(1);
514	<	uz_i = idat.eFrame1.getColumn(2);
512	>	ux_i = idat.eFrame1->getColumn(0);
513	>	uy_i = idat.eFrame1->getColumn(1);
514	>	uz_i = idat.eFrame1->getColumn(2);
515
516		cx_i = dot(ux_i, rhat);
517		cy_i = dot(uy_i, rhat);
#	Line 431 \| Line 522 \| namespace OpenMD {
522		duduz_i = V3Zero;
523		}
524
525	<	if (j_is_Charge)
526	<	q_j = data2.charge;
525	>	if (j_is_Charge) {
526	>	q_j = data2.fixedCharge;
527
528	+	if (j_is_Fluctuating)
529	+	q_j += *(idat.flucQ2);
530	+
531	+	if (idat.excluded) {
532	+	*(idat.skippedCharge1) += q_j;
533	+	}
534	+	}
535	+
536	+
537		if (j_is_Dipole) {
538		mu_j = data2.dipole_moment;
539	<	uz_j = idat.eFrame2.getColumn(2);
539	>	uz_j = idat.eFrame2->getColumn(2);
540
541		ct_j = dot(uz_j, rhat);
542
#	Line 452 \| Line 552 \| namespace OpenMD {
552		qyy_j = Q_j.y();
553		qzz_j = Q_j.z();
554
555	<	ux_j = idat.eFrame2.getColumn(0);
556	<	uy_j = idat.eFrame2.getColumn(1);
557	<	uz_j = idat.eFrame2.getColumn(2);
555	>	ux_j = idat.eFrame2->getColumn(0);
556	>	uy_j = idat.eFrame2->getColumn(1);
557	>	uz_j = idat.eFrame2->getColumn(2);
558
559		cx_j = dot(ux_j, rhat);
560		cy_j = dot(uy_j, rhat);
#	Line 465 \| Line 565 \| namespace OpenMD {
565		duduz_j = V3Zero;
566		}
567
568	+	if (i_is_Fluctuating && j_is_Fluctuating) {
569	+	J1 = Jij[idat.atypes];
570	+	J2 = Jij[make_pair(idat.atypes.second, idat.atypes.first)];
571	+	}
572	+
573		epot = 0.0;
574		dVdr = V3Zero;
575
#	Line 473 \| Line 578 \| namespace OpenMD {
578		if (j_is_Charge) {
579		if (screeningMethod_ == DAMPED) {
580		// assemble the damping variables
581	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
582	<	erfcVal = res.first;
583	<	derfcVal = res.second;
581	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
582	>	//erfcVal = res.first;
583	>	//derfcVal = res.second;
584	>
585	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
586	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
587	>
588		c1 = erfcVal * riji;
589		c2 = (-derfcVal + c1) * riji;
590		} else {
#	Line 483 \| Line 592 \| namespace OpenMD {
592		c2 = c1 * riji;
593		}
594
595	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
595	>	preVal = (idat.electroMult) pre11_;
596
597	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
597	>	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
598		vterm = preVal * (c1 - c1c_);
599	<	dudr = -idat.sw * preVal * c2;
599	>	dudr = - (idat.sw) preVal * c2;
600
601	<	} else if (summationMethod_ == SHIFTED_FORCE) {
602	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
603	<	dudr = idat.sw * preVal * (c2c_ - c2);
495	<
496	<	} else if (summationMethod_ == REACTION_FIELD) {
497	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
498	<	vterm = preVal * ( riji + rfVal );
499	<	dudr = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
601	>	} else if (summationMethod_ == esm_SHIFTED_FORCE) {
602	>	vterm = preVal * ( c1 - c1c_ + c2c_( (idat.rij) - cutoffRadius_) );
603	>	dudr = (idat.sw) preVal * (c2c_ - c2);
604
605	+	} else if (summationMethod_ == esm_REACTION_FIELD) {
606	+	rfVal = preRF_ * (idat.rij) *(idat.rij);
607	+
608	+	vterm = preVal * ( riji + rfVal );
609	+	dudr = (idat.sw) preVal * ( 2.0 * rfVal - riji ) * riji;
610	+
611	+	// if this is an excluded pair, there are still indirect
612	+	// interactions via the reaction field we must worry about:
613	+
614	+	if (idat.excluded) {
615	+	indirect_vpair += preVal * rfVal;
616	+	indirect_Pot += (idat.sw) preVal * rfVal;
617	+	indirect_dVdr += (idat.sw) preVal * two * rfVal * riji * rhat;
618	+	}
619	+
620		} else {
502	–	vterm = preVal * riji * erfcVal;
621
622	<	dudr = - idat.sw * preVal * c2;
622	>	vterm = preVal * riji * erfcVal;
623	>	dudr = - (idat.sw) preVal * c2;
624	>
625	>	}
626	>
627	>	vpair += vterm * q_i * q_j;
628	>	epot += (idat.sw) vterm * q_i * q_j;
629	>	dVdr += dudr * rhat * q_i * q_j;
630
631	+	if (i_is_Fluctuating) {
632	+	if (idat.excluded) {
633	+	// vFluc1 is the difference between the direct coulomb integral
634	+	// and the normal 1/r-like interaction between point charges.
635	+	coulInt = J1->getValueAt( *(idat.rij) );
636	+	vFluc1 = coulInt - ((idat.sw) vterm);
637	+	} else {
638	+	vFluc1 = 0.0;
639	+	}
640	+	(idat.dVdFQ1) += ( (idat.sw) * vterm + vFluc1 ) * q_j;
641		}
507	–
508	–	idat.vpair += vterm;
509	–	epot += idat.sw * vterm;
642
643	<	dVdr += dudr * rhat;
643	>	if (j_is_Fluctuating) {
644	>	if (idat.excluded) {
645	>	// vFluc2 is the difference between the direct coulomb integral
646	>	// and the normal 1/r-like interaction between point charges.
647	>	coulInt = J2->getValueAt( *(idat.rij) );
648	>	vFluc2 = coulInt - ((idat.sw) vterm);
649	>	} else {
650	>	vFluc2 = 0.0;
651	>	}
652	>	(idat.dVdFQ2) += ( (idat.sw) * vterm + vFluc2 ) * q_i;
653	>	}
654	>
655	>
656		}
657
658		if (j_is_Dipole) {
659		// pref is used by all the possible methods
660	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
661	<	preSw = idat.sw * pref;
660	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
661	>	preSw = (idat.sw) pref;
662
663	<	if (summationMethod_ == REACTION_FIELD) {
663	>	if (summationMethod_ == esm_REACTION_FIELD) {
664		ri2 = riji * riji;
665		ri3 = ri2 * riji;
666
667	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
668	<	idat.vpair += vterm;
669	<	epot += idat.sw * vterm;
667	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
668	>	vpair += vterm;
669	>	epot += (idat.sw) vterm;
670
671	<	dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
672	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
671	>	dVdr += -preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
672	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
673
674	+	// Even if we excluded this pair from direct interactions,
675	+	// we still have the reaction-field-mediated charge-dipole
676	+	// interaction:
677	+
678	+	if (idat.excluded) {
679	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
680	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
681	+	indirect_dVdr += preSw * preRF2_ * uz_j;
682	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
683	+	}
684	+
685		} else {
686		// determine the inverse r used if we have split dipoles
687		if (j_is_SplitDipole) {
688	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
688	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
689		ri = 1.0 / BigR;
690	<	scale = idat.rij * ri;
690	>	scale = (idat.rij) ri;
691		} else {
692		ri = riji;
693		scale = 1.0;
#	Line 542 \| Line 697 \| namespace OpenMD {
697
698		if (screeningMethod_ == DAMPED) {
699		// assemble the damping variables
700	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
701	<	erfcVal = res.first;
702	<	derfcVal = res.second;
700	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
701	>	//erfcVal = res.first;
702	>	//derfcVal = res.second;
703	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
704	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
705		c1 = erfcVal * ri;
706		c2 = (-derfcVal + c1) * ri;
707		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 559 \| Line 716 \| namespace OpenMD {
716		// calculate the potential
717		pot_term = scale * c2;
718		vterm = -pref * ct_j * pot_term;
719	<	idat.vpair += vterm;
720	<	epot += idat.sw * vterm;
719	>	vpair += vterm;
720	>	epot += (idat.sw) vterm;
721
722		// calculate derivatives for forces and torques
723
#	Line 568 \| Line 725 \| namespace OpenMD {
725		duduz_j += -preSw * pot_term * rhat;
726
727		}
728	+	if (i_is_Fluctuating) {
729	+	(idat.dVdFQ1) += ( (idat.sw) * vterm ) / q_i;
730	+	}
731		}
732
733		if (j_is_Quadrupole) {
#	Line 575 \| Line 735 \| namespace OpenMD {
735		cx2 = cx_j * cx_j;
736		cy2 = cy_j * cy_j;
737		cz2 = cz_j * cz_j;
738	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
738	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
739
740		if (screeningMethod_ == DAMPED) {
741		// assemble the damping variables
742	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
743	<	erfcVal = res.first;
744	<	derfcVal = res.second;
742	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
743	>	//erfcVal = res.first;
744	>	//derfcVal = res.second;
745	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
746	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
747		c1 = erfcVal * riji;
748		c2 = (-derfcVal + c1) * riji;
749		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 594 \| Line 756 \| namespace OpenMD {
756		}
757
758		// precompute variables for convenience
759	<	preSw = idat.sw * pref;
759	>	preSw = (idat.sw) pref;
760		c2ri = c2 * riji;
761		c3ri = c3 * riji;
762	<	c4rij = c4 * idat.rij;
763	<	rhatdot2 = 2.0 * rhat * c3;
762	>	c4rij = c4 * *(idat.rij) ;
763	>	rhatdot2 = two * rhat * c3;
764		rhatc4 = rhat * c4rij;
765
766		// calculate the potential
#	Line 606 \| Line 768 \| namespace OpenMD {
768		qyy_j * (cy2*c3 - c2ri) +
769		qzz_j * (cz2*c3 - c2ri) );
770		vterm = pref * pot_term;
771	<	idat.vpair += vterm;
772	<	epot += idat.sw * vterm;
771	>	vpair += vterm;
772	>	epot += (idat.sw) vterm;
773
774		// calculate derivatives for the forces and torques
775
776	<	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (2.0cx_jux_j + rhat)c3ri) +
777	<	qyy_j* (cy2rhatc4 - (2.0cy_juy_j + rhat)c3ri) +
778	<	qzz_j* (cz2rhatc4 - (2.0cz_juz_j + rhat)c3ri));
776	>	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (twocx_jux_j + rhat)c3ri) +
777	>	qyy_j* (cy2rhatc4 - (twocy_juy_j + rhat)c3ri) +
778	>	qzz_j* (cz2rhatc4 - (twocz_juz_j + rhat)c3ri));
779
780		dudux_j += preSw * qxx_j * cx_j * rhatdot2;
781		duduy_j += preSw * qyy_j * cy_j * rhatdot2;
782		duduz_j += preSw * qzz_j * cz_j * rhatdot2;
783	+	if (i_is_Fluctuating) {
784	+	(idat.dVdFQ1) += ( (idat.sw) * vterm ) / q_i;
785	+	}
786	+
787		}
788		}
789
#	Line 625 \| Line 791 \| namespace OpenMD {
791
792		if (j_is_Charge) {
793		// variables used by all the methods
794	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
795	<	preSw = idat.sw * pref;
794	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
795	>	preSw = (idat.sw) pref;
796
797	<	if (summationMethod_ == REACTION_FIELD) {
797	>	if (summationMethod_ == esm_REACTION_FIELD) {
798
799		ri2 = riji * riji;
800		ri3 = ri2 * riji;
801
802	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
803	<	idat.vpair += vterm;
804	<	epot += idat.sw * vterm;
802	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
803	>	vpair += vterm;
804	>	epot += (idat.sw) vterm;
805
806	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
806	>	dVdr += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_ * uz_i);
807
808	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
808	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
809	>
810	>	// Even if we excluded this pair from direct interactions,
811	>	// we still have the reaction-field-mediated charge-dipole
812	>	// interaction:
813	>
814	>	if (idat.excluded) {
815	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
816	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
817	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
818	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
819	>	}
820
821		} else {
822
823		// determine inverse r if we are using split dipoles
824		if (i_is_SplitDipole) {
825	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
825	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
826		ri = 1.0 / BigR;
827	<	scale = idat.rij * ri;
827	>	scale = (idat.rij) ri;
828		} else {
829		ri = riji;
830		scale = 1.0;
#	Line 657 \| Line 834 \| namespace OpenMD {
834
835		if (screeningMethod_ == DAMPED) {
836		// assemble the damping variables
837	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
838	<	erfcVal = res.first;
839	<	derfcVal = res.second;
837	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
838	>	//erfcVal = res.first;
839	>	//derfcVal = res.second;
840	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
841	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
842		c1 = erfcVal * ri;
843		c2 = (-derfcVal + c1) * ri;
844		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 674 \| Line 853 \| namespace OpenMD {
853		// calculate the potential
854		pot_term = c2 * scale;
855		vterm = pref * ct_i * pot_term;
856	<	idat.vpair += vterm;
857	<	epot += idat.sw * vterm;
856	>	vpair += vterm;
857	>	epot += (idat.sw) vterm;
858
859		// calculate derivatives for the forces and torques
860		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
861		duduz_i += preSw * pot_term * rhat;
862		}
863	+
864	+	if (j_is_Fluctuating) {
865	+	(idat.dVdFQ2) += ( (idat.sw) * vterm ) / q_j;
866	+	}
867	+
868		}
869
870		if (j_is_Dipole) {
871		// variables used by all methods
872		ct_ij = dot(uz_i, uz_j);
873
874	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
875	<	preSw = idat.sw * pref;
874	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
875	>	preSw = (idat.sw) pref;
876
877	<	if (summationMethod_ == REACTION_FIELD) {
877	>	if (summationMethod_ == esm_REACTION_FIELD) {
878		ri2 = riji * riji;
879		ri3 = ri2 * riji;
880		ri4 = ri2 * ri2;
881
882		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
883		preRF2_ * ct_ij );
884	<	idat.vpair += vterm;
885	<	epot += idat.sw * vterm;
884	>	vpair += vterm;
885	>	epot += (idat.sw) vterm;
886
887		a1 = 5.0 * ct_i * ct_j - ct_ij;
888
889	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
889	>	dVdr += preSw * three * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
890
891	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
892	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
891	>	duduz_i += preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
892	>	duduz_j += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_*uz_i);
893
894	+	if (idat.excluded) {
895	+	indirect_vpair += - pref * preRF2_ * ct_ij;
896	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
897	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
898	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
899	+	}
900	+
901		} else {
902
903		if (i_is_SplitDipole) {
904		if (j_is_SplitDipole) {
905	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
905	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
906		} else {
907	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
907	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
908		}
909		ri = 1.0 / BigR;
910	<	scale = idat.rij * ri;
910	>	scale = (idat.rij) ri;
911		} else {
912		if (j_is_SplitDipole) {
913	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
913	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
914		ri = 1.0 / BigR;
915	<	scale = idat.rij * ri;
915	>	scale = (idat.rij) ri;
916		} else {
917		ri = riji;
918		scale = 1.0;
#	Line 729 \| Line 920 \| namespace OpenMD {
920		}
921		if (screeningMethod_ == DAMPED) {
922		// assemble damping variables
923	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
924	<	erfcVal = res.first;
925	<	derfcVal = res.second;
923	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
924	>	//erfcVal = res.first;
925	>	//derfcVal = res.second;
926	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
927	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
928		c1 = erfcVal * ri;
929		c2 = (-derfcVal + c1) * ri;
930		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 751 \| Line 944 \| namespace OpenMD {
944		preSwSc = preSw * scale;
945		c2ri = c2 * ri;
946		c3ri = c3 * ri;
947	<	c4rij = c4 * idat.rij;
947	>	c4rij = c4 * *(idat.rij) ;
948
949		// calculate the potential
950		pot_term = (ct_ij * c2ri - ctidotj * c3);
951		vterm = pref * pot_term;
952	<	idat.vpair += vterm;
953	<	epot += idat.sw * vterm;
952	>	vpair += vterm;
953	>	epot += (idat.sw) vterm;
954
955		// calculate derivatives for the forces and torques
956		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 776 \| Line 969 \| namespace OpenMD {
969		cy2 = cy_i * cy_i;
970		cz2 = cz_i * cz_i;
971
972	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
972	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
973
974		if (screeningMethod_ == DAMPED) {
975		// assemble the damping variables
976	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
977	<	erfcVal = res.first;
978	<	derfcVal = res.second;
976	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
977	>	//erfcVal = res.first;
978	>	//derfcVal = res.second;
979	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
980	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
981		c1 = erfcVal * riji;
982		c2 = (-derfcVal + c1) * riji;
983		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 795 \| Line 990 \| namespace OpenMD {
990		}
991
992		// precompute some variables for convenience
993	<	preSw = idat.sw * pref;
993	>	preSw = (idat.sw) pref;
994		c2ri = c2 * riji;
995		c3ri = c3 * riji;
996	<	c4rij = c4 * idat.rij;
997	<	rhatdot2 = 2.0 * rhat * c3;
996	>	c4rij = c4 * *(idat.rij) ;
997	>	rhatdot2 = two * rhat * c3;
998		rhatc4 = rhat * c4rij;
999
1000		// calculate the potential
#	Line 808 \| Line 1003 \| namespace OpenMD {
1003		qzz_i * (cz2 * c3 - c2ri) );
1004
1005		vterm = pref * pot_term;
1006	<	idat.vpair += vterm;
1007	<	epot += idat.sw * vterm;
1006	>	vpair += vterm;
1007	>	epot += (idat.sw) vterm;
1008
1009		// calculate the derivatives for the forces and torques
1010
1011	<	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (2.0cx_iux_i + rhat)c3ri) +
1012	<	qyy_i* (cy2rhatc4 - (2.0cy_iuy_i + rhat)c3ri) +
1013	<	qzz_i* (cz2rhatc4 - (2.0cz_iuz_i + rhat)c3ri));
1011	>	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (twocx_iux_i + rhat)c3ri) +
1012	>	qyy_i* (cy2rhatc4 - (twocy_iuy_i + rhat)c3ri) +
1013	>	qzz_i* (cz2rhatc4 - (twocz_iuz_i + rhat)c3ri));
1014
1015		dudux_i += preSw * qxx_i * cx_i * rhatdot2;
1016		duduy_i += preSw * qyy_i * cy_i * rhatdot2;
1017		duduz_i += preSw * qzz_i * cz_i * rhatdot2;
823	–	}
824	–	}
1018
1019	<	idat.pot += epot;
1020	<	idat.f1 += dVdr;
1019	>	if (j_is_Fluctuating) {
1020	>	(idat.dVdFQ2) += ( (idat.sw) * vterm ) / q_j;
1021	>	}
1022
1023	<	if (i_is_Dipole \|\| i_is_Quadrupole)
830	<	idat.t1 -= cross(uz_i, duduz_i);
831	<	if (i_is_Quadrupole) {
832	<	idat.t1 -= cross(ux_i, dudux_i);
833	<	idat.t1 -= cross(uy_i, duduy_i);
1023	>	}
1024		}
1025
836	–	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	–	}
1026
1027	<	return;
1028	<	}
1027	>	if (!idat.excluded) {
1028	>	*(idat.vpair) += vpair;
1029	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
1030	>	*(idat.f1) += dVdr;
1031	>
1032	>	if (i_is_Dipole \|\| i_is_Quadrupole)
1033	>	*(idat.t1) -= cross(uz_i, duduz_i);
1034	>	if (i_is_Quadrupole) {
1035	>	*(idat.t1) -= cross(ux_i, dudux_i);
1036	>	*(idat.t1) -= cross(uy_i, duduy_i);
1037	>	}
1038	>
1039	>	if (j_is_Dipole \|\| j_is_Quadrupole)
1040	>	*(idat.t2) -= cross(uz_j, duduz_j);
1041	>	if (j_is_Quadrupole) {
1042	>	*(idat.t2) -= cross(uz_j, dudux_j);
1043	>	*(idat.t2) -= cross(uz_j, duduy_j);
1044	>	}
1045
1046	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
1046	>	} else {
1047
1048	<	if (!initialized_) initialize();
1049	<
850	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
851	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
852	<
853	<	// logicals
1048	>	// only accumulate the forces and torques resulting from the
1049	>	// indirect reaction field terms.
1050
1051	<	bool i_is_Charge = data1.is_Charge;
1052	<	bool i_is_Dipole = data1.is_Dipole;
1053	<
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:
1051	>	*(idat.vpair) += indirect_vpair;
1052	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
1053	>	*(idat.f1) += indirect_dVdr;
1054
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	–
1055		if (i_is_Dipole)
1056	<	skdat.t1 -= cross(uz_i, duduz_i);
1056	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
1057		if (j_is_Dipole)
1058	<	skdat.t2 -= cross(uz_j, duduz_j);
1058	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
1059		}
1060	<	}
1060	>
1061	>	return;
1062	>	}
1063
1064	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1065	<	RealType mu1, preVal, chg1, self;
949	<
1064	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1065	>	RealType mu1, preVal, self;
1066		if (!initialized_) initialize();
1067	<
1068	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1067	>
1068	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1069
1070		// logicals
955	–
1071		bool i_is_Charge = data.is_Charge;
1072		bool i_is_Dipole = data.is_Dipole;
1073	+	bool i_is_Fluctuating = data.is_Fluctuating;
1074	+	RealType chg1 = data.fixedCharge;
1075	+
1076	+	if (i_is_Fluctuating) {
1077	+	chg1 += *(sdat.flucQ);
1078	+	// dVdFQ is really a force, so this is negative the derivative
1079	+	(sdat.dVdFQ) -= (sdat.flucQ) * data.hardness + data.electronegativity;
1080	+	}
1081
1082	<	if (summationMethod_ == REACTION_FIELD) {
1082	>	if (summationMethod_ == esm_REACTION_FIELD) {
1083		if (i_is_Dipole) {
1084		mu1 = data.dipole_moment;
1085		preVal = pre22_ * preRF2_ * mu1 * mu1;
1086	<	scdat.pot -= 0.5 * preVal;
1086	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1087
1088		// The self-correction term adds into the reaction field vector
1089	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1089	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1090		Vector3d ei = preVal * uz_i;
1091
1092		// This looks very wrong. A vector crossed with itself is zero.
1093	<	scdat.t -= cross(uz_i, ei);
1093	>	*(sdat.t) -= cross(uz_i, ei);
1094		}
1095	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1095	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1096		if (i_is_Charge) {
974	–	chg1 = data.charge;
1097		if (screeningMethod_ == DAMPED) {
1098	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1098	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1099		} else {
1100	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1100	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1101		}
1102	<	scdat.pot += self;
1102	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1103		}
1104		}
1105		}
1106
1107	<	RealType Electrostatic::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
1107	>	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1108		// This seems to work moderately well as a default. There's no
1109		// inherent scale for 1/r interactions that we can standardize.
1110		// 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 1750 by gezelter, Thu Jun 7 12:53:46 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 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC