[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 1721 by gezelter, Thu May 24 14:17:42 2012 UTC

#	Line 34 \| Line 34
34		* work. Good starting points are:
35		*
36		* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	<	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	>	* [2] Fennell & Gezelter, J. Chem. Phys. 124 234104 (2006).
38		* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4] Vardeman & Gezelter, in progress (2009).
39	>	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	>	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stdio.h>
#	Line 46 \| Line 47
47		#include "nonbonded/Electrostatic.hpp"
48		#include "utils/simError.h"
49		#include "types/NonBondedInteractionType.hpp"
50	<	#include "types/DirectionalAtomType.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52	>	#include "types/MultipoleAdapter.hpp"
53	>	#include "io/Globals.hpp"
54	>	#include "nonbonded/SlaterIntegrals.hpp"
55	>	#include "utils/PhysicalConstants.hpp"
56
57
58		namespace OpenMD {
59
60		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
61	<	forceField_(NULL) {}
61	>	forceField_(NULL), info_(NULL),
62	>	haveCutoffRadius_(false),
63	>	haveDampingAlpha_(false),
64	>	haveDielectric_(false),
65	>	haveElectroSpline_(false)
66	>	{}
67
68		void Electrostatic::initialize() {
69	+
70	+	Globals* simParams_ = info_->getSimParams();
71	+
72	+	summationMap_["HARD"] = esm_HARD;
73	+	summationMap_["NONE"] = esm_HARD;
74	+	summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
75	+	summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL;
76	+	summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE;
77	+	summationMap_["REACTION_FIELD"] = esm_REACTION_FIELD;
78	+	summationMap_["EWALD_FULL"] = esm_EWALD_FULL;
79	+	summationMap_["EWALD_PME"] = esm_EWALD_PME;
80	+	summationMap_["EWALD_SPME"] = esm_EWALD_SPME;
81	+	screeningMap_["DAMPED"] = DAMPED;
82	+	screeningMap_["UNDAMPED"] = UNDAMPED;
83	+
84		// these prefactors convert the multipole interactions into kcal / mol
85		// all were computed assuming distances are measured in angstroms
86		// Charge-Charge, assuming charges are measured in electrons
#	Line 79 \| Line 105 \| namespace OpenMD {
105
106		// variables to handle different summation methods for long-range
107		// electrostatics:
108	<	summationMethod_ = NONE;
108	>	summationMethod_ = esm_HARD;
109		screeningMethod_ = UNDAMPED;
110		dielectric_ = 1.0;
111		one_third_ = 1.0 / 3.0;
86	–	haveDefaultCutoff_ = false;
87	–	haveDampingAlpha_ = false;
88	–	haveDielectric_ = false;
89	–	haveElectroSpline_ = false;
112
113	+	// check the summation method:
114	+	if (simParams_->haveElectrostaticSummationMethod()) {
115	+	string myMethod = simParams_->getElectrostaticSummationMethod();
116	+	toUpper(myMethod);
117	+	map<string, ElectrostaticSummationMethod>::iterator i;
118	+	i = summationMap_.find(myMethod);
119	+	if ( i != summationMap_.end() ) {
120	+	summationMethod_ = (*i).second;
121	+	} else {
122	+	// throw error
123	+	sprintf( painCave.errMsg,
124	+	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
125	+	"\t(Input file specified %s .)\n"
126	+	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
127	+	"\t\"shifted_potential\", \"shifted_force\", or \n"
128	+	"\t\"reaction_field\".\n", myMethod.c_str() );
129	+	painCave.isFatal = 1;
130	+	simError();
131	+	}
132	+	} else {
133	+	// set ElectrostaticSummationMethod to the cutoffMethod:
134	+	if (simParams_->haveCutoffMethod()){
135	+	string myMethod = simParams_->getCutoffMethod();
136	+	toUpper(myMethod);
137	+	map<string, ElectrostaticSummationMethod>::iterator i;
138	+	i = summationMap_.find(myMethod);
139	+	if ( i != summationMap_.end() ) {
140	+	summationMethod_ = (*i).second;
141	+	}
142	+	}
143	+	}
144	+
145	+	if (summationMethod_ == esm_REACTION_FIELD) {
146	+	if (!simParams_->haveDielectric()) {
147	+	// throw warning
148	+	sprintf( painCave.errMsg,
149	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
150	+	"\tA default value of %f will be used for the dielectric.\n", dielectric_);
151	+	painCave.isFatal = 0;
152	+	painCave.severity = OPENMD_INFO;
153	+	simError();
154	+	} else {
155	+	dielectric_ = simParams_->getDielectric();
156	+	}
157	+	haveDielectric_ = true;
158	+	}
159	+
160	+	if (simParams_->haveElectrostaticScreeningMethod()) {
161	+	string myScreen = simParams_->getElectrostaticScreeningMethod();
162	+	toUpper(myScreen);
163	+	map<string, ElectrostaticScreeningMethod>::iterator i;
164	+	i = screeningMap_.find(myScreen);
165	+	if ( i != screeningMap_.end()) {
166	+	screeningMethod_ = (*i).second;
167	+	} else {
168	+	sprintf( painCave.errMsg,
169	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
170	+	"\t(Input file specified %s .)\n"
171	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
172	+	"or \"damped\".\n", myScreen.c_str() );
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	}
177	+
178	+	// check to make sure a cutoff value has been set:
179	+	if (!haveCutoffRadius_) {
180	+	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
181	+	"Cutoff value!\n");
182	+	painCave.severity = OPENMD_ERROR;
183	+	painCave.isFatal = 1;
184	+	simError();
185	+	}
186	+
187	+	if (screeningMethod_ == DAMPED) {
188	+	if (!simParams_->haveDampingAlpha()) {
189	+	// first set a cutoff dependent alpha value
190	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
191	+	dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
192	+	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
193	+
194	+	// throw warning
195	+	sprintf( painCave.errMsg,
196	+	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
197	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
198	+	dampingAlpha_, cutoffRadius_);
199	+	painCave.severity = OPENMD_INFO;
200	+	painCave.isFatal = 0;
201	+	simError();
202	+	} else {
203	+	dampingAlpha_ = simParams_->getDampingAlpha();
204	+	}
205	+	haveDampingAlpha_ = true;
206	+	}
207	+
208		// find all of the Electrostatic atom Types:
209		ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
210		ForceField::AtomTypeContainer::MapTypeIterator i;
211		AtomType* at;
212	<
212	>
213		for (at = atomTypes->beginType(i); at != NULL;
214		at = atomTypes->nextType(i)) {
215
#	Line 100 \| Line 217 \| namespace OpenMD {
217		addType(at);
218		}
219
103	–	// check to make sure a cutoff value has been set:
104	–	if (!haveDefaultCutoff_) {
105	–	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
106	–	"Cutoff value!\n");
107	–	painCave.severity = OPENMD_ERROR;
108	–	painCave.isFatal = 1;
109	–	simError();
110	–	}
220
221	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
222	<	rcuti_ = 1.0 / defaultCutoff_;
221	>	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
222	>	rcuti_ = 1.0 / cutoffRadius_;
223		rcuti2_ = rcuti_ * rcuti_;
224		rcuti3_ = rcuti2_ * rcuti_;
225		rcuti4_ = rcuti2_ * rcuti2_;
226
227		if (screeningMethod_ == DAMPED) {
228	<	if (!haveDampingAlpha_) {
120	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no "
121	<	"DampingAlpha value!\n");
122	<	painCave.severity = OPENMD_ERROR;
123	<	painCave.isFatal = 1;
124	<	simError();
125	<	}
126	<
228	>
229		alpha2_ = dampingAlpha_ * dampingAlpha_;
230		alpha4_ = alpha2_ * alpha2_;
231		alpha6_ = alpha4_ * alpha2_;
232		alpha8_ = alpha4_ * alpha4_;
233
234	<	constEXP_ = exp(-alpha2_ * defaultCutoff2_);
234	>	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
235		invRootPi_ = 0.56418958354775628695;
236		alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
237
238	<	c1c_ = erfc(dampingAlpha_ * defaultCutoff_) * rcuti_;
238	>	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
239		c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
240		c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
241		c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
#	Line 148 \| Line 250 \| namespace OpenMD {
250		c6c_ = 9.0 * c5c_ * rcuti2_;
251		}
252
253	<	if (summationMethod_ == REACTION_FIELD) {
254	<	if (haveDielectric_) {
255	<	preRF_ = (dielectric_ - 1.0) /
256	<	((2.0 * dielectric_ + 1.0) * defaultCutoff2_ * defaultCutoff_);
155	<	preRF2_ = 2.0 * preRF_;
156	<	} else {
157	<	sprintf( painCave.errMsg, "Electrostatic::initialize has no Dielectric"
158	<	" value!\n");
159	<	painCave.severity = OPENMD_ERROR;
160	<	painCave.isFatal = 1;
161	<	simError();
162	<	}
253	>	if (summationMethod_ == esm_REACTION_FIELD) {
254	>	preRF_ = (dielectric_ - 1.0) /
255	>	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
256	>	preRF2_ = 2.0 * preRF_;
257		}
258	<
259	<	RealType dx = defaultCutoff_ / RealType(np_ - 1);
258	>
259	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
260	>	// have charged atoms longer than the cutoffRadius away from each
261	>	// other. Splining may not be the best choice here. Direct calls
262	>	// to erfc might be preferrable.
263	>
264	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
265		RealType rval;
266		vector<RealType> rvals;
267		vector<RealType> yvals;
#	Line 186 \| Line 285 \| namespace OpenMD {
285		electrostaticAtomData.is_SplitDipole = false;
286		electrostaticAtomData.is_Quadrupole = false;
287
288	<	if (atomType->isCharge()) {
190	<	GenericData* data = atomType->getPropertyByName("Charge");
288	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
289
290	<	if (data == NULL) {
193	<	sprintf( painCave.errMsg, "Electrostatic::addType could not find "
194	<	"Charge\n"
195	<	"\tparameters for atomType %s.\n",
196	<	atomType->getName().c_str());
197	<	painCave.severity = OPENMD_ERROR;
198	<	painCave.isFatal = 1;
199	<	simError();
200	<	}
201	<
202	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
203	<	if (doubleData == NULL) {
204	<	sprintf( painCave.errMsg,
205	<	"Electrostatic::addType could not convert GenericData to "
206	<	"Charge for\n"
207	<	"\tatom type %s\n", atomType->getName().c_str());
208	<	painCave.severity = OPENMD_ERROR;
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
290	>	if (fca.isFixedCharge()) {
291		electrostaticAtomData.is_Charge = true;
292	<	electrostaticAtomData.charge = doubleData->getData();
292	>	electrostaticAtomData.fixedCharge = fca.getCharge();
293		}
294
295	<	if (atomType->isDirectional()) {
296	<	DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
297	<
298	<	if (daType->isDipole()) {
299	<	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	<	}
242	<	electrostaticAtomData.is_Dipole = true;
243	<	electrostaticAtomData.dipole_moment = doubleData->getData();
295	>	MultipoleAdapter ma = MultipoleAdapter(atomType);
296	>	if (ma.isMultipole()) {
297	>	if (ma.isDipole()) {
298	>	electrostaticAtomData.is_Dipole = true;
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	+	} else {
325	+	electrostaticAtomData.is_Fluctuating = false;
326	+	}
327	+
328		pair<map<int,AtomType*>::iterator,bool> ret;
329	<	ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) );
329	>	ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
330	>	atomType) );
331		if (ret.second == false) {
332		sprintf( painCave.errMsg,
333		"Electrostatic already had a previous entry with ident %d\n",
334	<	atp.ident);
334	>	atomType->getIdent() );
335		painCave.severity = OPENMD_INFO;
336		painCave.isFatal = 0;
337		simError();
338		}
339
340	<	ElectrostaticMap[atomType] = electrostaticAtomData;
340	>	ElectrostaticMap[atomType] = electrostaticAtomData;
341	>
342	>	// Now, iterate over all known types and add to the mixing map:
343	>
344	>	map<AtomType*, ElectrostaticAtomData>::iterator it;
345	>	for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
346	>	AtomType* atype2 = (*it).first;
347	>	ElectrostaticAtomData eaData2 = (*it).second;
348	>	if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) {
349	>
350	>	RealType a = electrostaticAtomData.slaterZeta;
351	>	RealType b = eaData2.slaterZeta;
352	>	int m = electrostaticAtomData.slaterN;
353	>	int n = eaData2.slaterN;
354	>
355	>	// Create the spline of the coulombic integral for s-type
356	>	// Slater orbitals. Add a 2 angstrom safety window to deal
357	>	// with cutoffGroups that have charged atoms longer than the
358	>	// cutoffRadius away from each other.
359	>
360	>	RealType rval;
361	>	RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
362	>	vector<RealType> rvals;
363	>	vector<RealType> J1vals;
364	>	vector<RealType> J2vals;
365	>	for (int i = 0; i < np_; i++) {
366	>	rval = RealType(i) * dr;
367	>	rvals.push_back(rval);
368	>	J1vals.push_back( sSTOCoulInt( a, b, m, n, rval * PhysicalConstants::angstromsToBohr ) );
369	>	// may not be necessary if Slater coulomb integral is symmetric
370	>	J2vals.push_back( sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) );
371	>	}
372	>
373	>	CubicSpline* J1 = new CubicSpline();
374	>	J1->addPoints(rvals, J1vals);
375	>	CubicSpline* J2 = new CubicSpline();
376	>	J2->addPoints(rvals, J2vals);
377	>
378	>	pair<AtomType, AtomType> key1, key2;
379	>	key1 = make_pair(atomType, atype2);
380	>	key2 = make_pair(atype2, atomType);
381	>
382	>	Jij[key1] = J1;
383	>	Jij[key2] = J2;
384	>	}
385	>	}
386	>
387		return;
388		}
389
390	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
391	<	RealType theRSW ) {
392	<	defaultCutoff_ = theECR;
393	<	rrf_ = defaultCutoff_;
322	<	rt_ = theRSW;
323	<	haveDefaultCutoff_ = true;
390	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
391	>	cutoffRadius_ = rCut;
392	>	rrf_ = cutoffRadius_;
393	>	haveCutoffRadius_ = true;
394		}
395	+
396	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
397	+	rt_ = rSwitch;
398	+	}
399		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
400		summationMethod_ = esm;
401		}
#	Line 337 \| Line 411 \| namespace OpenMD {
411		haveDielectric_ = true;
412		}
413
414	<	void Electrostatic::calcForce(InteractionData idat) {
414	>	void Electrostatic::calcForce(InteractionData &idat) {
415
416		// utility variables. Should clean these up and use the Vector3d and
417		// Mat3x3d to replace as many as we can in future versions:
#	Line 351 \| Line 425 \| namespace OpenMD {
425		RealType ct_i, ct_j, ct_ij, a1;
426		RealType riji, ri, ri2, ri3, ri4;
427		RealType pref, vterm, epot, dudr;
428	+	RealType vpair(0.0);
429		RealType scale, sc2;
430		RealType pot_term, preVal, rfVal;
431		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
432		RealType preSw, preSwSc;
433		RealType c1, c2, c3, c4;
434	<	RealType erfcVal, derfcVal;
434	>	RealType erfcVal(1.0), derfcVal(0.0);
435		RealType BigR;
436	+	RealType two(2.0), three(3.0);
437
438		Vector3d Q_i, Q_j;
439		Vector3d ux_i, uy_i, uz_i;
#	Line 367 \| Line 443 \| namespace OpenMD {
443		Vector3d rhatdot2, rhatc4;
444		Vector3d dVdr;
445
446	+	// variables for indirect (reaction field) interactions for excluded pairs:
447	+	RealType indirect_Pot(0.0);
448	+	RealType indirect_vpair(0.0);
449	+	Vector3d indirect_dVdr(V3Zero);
450	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
451	+
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 385 \| 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 412 \| 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 425 \| 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 (i_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 446 \| 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 459 \| 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 467 \| 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 477 \| Line 592 \| namespace OpenMD {
592		c2 = c1 * riji;
593		}
594
595	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
595	>	preVal = (idat.electroMult) pre11_ * q_i * q_j;
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);
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_ == REACTION_FIELD) {
606	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
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;
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 {
496	–	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	+
628	+	if (i_is_Fluctuating) {
629	+	if (!idat.excluded)
630	+	(idat.dVdFQ1) += (idat.sw) * vterm / q_i;
631	+	else {
632	+	res = J1->getValueAndDerivativeAt( *(idat.rij) );
633	+	(idat.dVdFQ1) += pre11_ res.first * q_j;
634	+	}
635		}
636	<
637	<	idat.vpair += vterm;
638	<	epot += idat.sw * vterm;
636	>	if (j_is_Fluctuating) {
637	>	if (!idat.excluded)
638	>	(idat.dVdFQ2) += (idat.sw) * vterm / q_j;
639	>	else {
640	>	res = J2->getValueAndDerivativeAt( *(idat.rij) );
641	>	(idat.dVdFQ2) += pre11_ res.first * q_i;
642	>	}
643	>	}
644
645	<	dVdr += dudr * rhat;
645	>	vpair += vterm;
646	>	epot += (idat.sw) vterm;
647	>	dVdr += dudr * rhat;
648		}
649
650		if (j_is_Dipole) {
651		// pref is used by all the possible methods
652	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
653	<	preSw = idat.sw * pref;
652	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
653	>	preSw = (idat.sw) pref;
654
655	<	if (summationMethod_ == REACTION_FIELD) {
655	>	if (summationMethod_ == esm_REACTION_FIELD) {
656		ri2 = riji * riji;
657		ri3 = ri2 * riji;
658
659	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
660	<	idat.vpair += vterm;
661	<	epot += idat.sw * vterm;
659	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
660	>	vpair += vterm;
661	>	epot += (idat.sw) vterm;
662
663	<	dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
664	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
663	>	dVdr += -preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
664	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
665
666	+	// Even if we excluded this pair from direct interactions,
667	+	// we still have the reaction-field-mediated charge-dipole
668	+	// interaction:
669	+
670	+	if (idat.excluded) {
671	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
672	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
673	+	indirect_dVdr += preSw * preRF2_ * uz_j;
674	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
675	+	}
676	+
677		} else {
678		// determine the inverse r used if we have split dipoles
679		if (j_is_SplitDipole) {
680	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
680	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
681		ri = 1.0 / BigR;
682	<	scale = idat.rij * ri;
682	>	scale = (idat.rij) ri;
683		} else {
684		ri = riji;
685		scale = 1.0;
#	Line 536 \| Line 689 \| namespace OpenMD {
689
690		if (screeningMethod_ == DAMPED) {
691		// assemble the damping variables
692	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
693	<	erfcVal = res.first;
694	<	derfcVal = res.second;
692	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
693	>	//erfcVal = res.first;
694	>	//derfcVal = res.second;
695	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
696	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
697		c1 = erfcVal * ri;
698		c2 = (-derfcVal + c1) * ri;
699		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 553 \| Line 708 \| namespace OpenMD {
708		// calculate the potential
709		pot_term = scale * c2;
710		vterm = -pref * ct_j * pot_term;
711	<	idat.vpair += vterm;
712	<	epot += idat.sw * vterm;
711	>	vpair += vterm;
712	>	epot += (idat.sw) vterm;
713
714		// calculate derivatives for forces and torques
715
#	Line 569 \| Line 724 \| namespace OpenMD {
724		cx2 = cx_j * cx_j;
725		cy2 = cy_j * cy_j;
726		cz2 = cz_j * cz_j;
727	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
727	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
728
729		if (screeningMethod_ == DAMPED) {
730		// assemble the damping variables
731	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
732	<	erfcVal = res.first;
733	<	derfcVal = res.second;
731	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
732	>	//erfcVal = res.first;
733	>	//derfcVal = res.second;
734	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
735	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
736		c1 = erfcVal * riji;
737		c2 = (-derfcVal + c1) * riji;
738		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 588 \| Line 745 \| namespace OpenMD {
745		}
746
747		// precompute variables for convenience
748	<	preSw = idat.sw * pref;
748	>	preSw = (idat.sw) pref;
749		c2ri = c2 * riji;
750		c3ri = c3 * riji;
751	<	c4rij = c4 * idat.rij;
752	<	rhatdot2 = 2.0 * rhat * c3;
751	>	c4rij = c4 * *(idat.rij) ;
752	>	rhatdot2 = two * rhat * c3;
753		rhatc4 = rhat * c4rij;
754
755		// calculate the potential
#	Line 600 \| Line 757 \| namespace OpenMD {
757		qyy_j * (cy2*c3 - c2ri) +
758		qzz_j * (cz2*c3 - c2ri) );
759		vterm = pref * pot_term;
760	<	idat.vpair += vterm;
761	<	epot += idat.sw * vterm;
760	>	vpair += vterm;
761	>	epot += (idat.sw) vterm;
762
763		// calculate derivatives for the forces and torques
764
765	<	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (2.0cx_jux_j + rhat)c3ri) +
766	<	qyy_j* (cy2rhatc4 - (2.0cy_juy_j + rhat)c3ri) +
767	<	qzz_j* (cz2rhatc4 - (2.0cz_juz_j + rhat)c3ri));
765	>	dVdr += -preSw * ( qxx_j* (cx2rhatc4 - (twocx_jux_j + rhat)c3ri) +
766	>	qyy_j* (cy2rhatc4 - (twocy_juy_j + rhat)c3ri) +
767	>	qzz_j* (cz2rhatc4 - (twocz_juz_j + rhat)c3ri));
768
769		dudux_j += preSw * qxx_j * cx_j * rhatdot2;
770		duduy_j += preSw * qyy_j * cy_j * rhatdot2;
#	Line 619 \| Line 776 \| namespace OpenMD {
776
777		if (j_is_Charge) {
778		// variables used by all the methods
779	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
780	<	preSw = idat.sw * pref;
779	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
780	>	preSw = (idat.sw) pref;
781
782	<	if (summationMethod_ == REACTION_FIELD) {
782	>	if (summationMethod_ == esm_REACTION_FIELD) {
783
784		ri2 = riji * riji;
785		ri3 = ri2 * riji;
786
787	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
788	<	idat.vpair += vterm;
789	<	epot += idat.sw * vterm;
787	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
788	>	vpair += vterm;
789	>	epot += (idat.sw) vterm;
790
791	<	dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
791	>	dVdr += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_ * uz_i);
792
793	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
793	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
794	>
795	>	// Even if we excluded this pair from direct interactions,
796	>	// we still have the reaction-field-mediated charge-dipole
797	>	// interaction:
798	>
799	>	if (idat.excluded) {
800	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
801	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
802	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
803	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
804	>	}
805
806		} else {
807
808		// determine inverse r if we are using split dipoles
809		if (i_is_SplitDipole) {
810	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
810	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
811		ri = 1.0 / BigR;
812	<	scale = idat.rij * ri;
812	>	scale = (idat.rij) ri;
813		} else {
814		ri = riji;
815		scale = 1.0;
#	Line 651 \| Line 819 \| namespace OpenMD {
819
820		if (screeningMethod_ == DAMPED) {
821		// assemble the damping variables
822	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
823	<	erfcVal = res.first;
824	<	derfcVal = res.second;
822	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
823	>	//erfcVal = res.first;
824	>	//derfcVal = res.second;
825	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
826	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
827		c1 = erfcVal * ri;
828		c2 = (-derfcVal + c1) * ri;
829		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 668 \| Line 838 \| namespace OpenMD {
838		// calculate the potential
839		pot_term = c2 * scale;
840		vterm = pref * ct_i * pot_term;
841	<	idat.vpair += vterm;
842	<	epot += idat.sw * vterm;
841	>	vpair += vterm;
842	>	epot += (idat.sw) vterm;
843
844		// calculate derivatives for the forces and torques
845		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
#	Line 681 \| Line 851 \| namespace OpenMD {
851		// variables used by all methods
852		ct_ij = dot(uz_i, uz_j);
853
854	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
855	<	preSw = idat.sw * pref;
854	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
855	>	preSw = (idat.sw) pref;
856
857	<	if (summationMethod_ == REACTION_FIELD) {
857	>	if (summationMethod_ == esm_REACTION_FIELD) {
858		ri2 = riji * riji;
859		ri3 = ri2 * riji;
860		ri4 = ri2 * ri2;
861
862		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
863		preRF2_ * ct_ij );
864	<	idat.vpair += vterm;
865	<	epot += idat.sw * vterm;
864	>	vpair += vterm;
865	>	epot += (idat.sw) vterm;
866
867		a1 = 5.0 * ct_i * ct_j - ct_ij;
868
869	<	dVdr += preSw * 3.0 * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
869	>	dVdr += preSw * three * ri4 * (a1 * rhat - ct_i * uz_j - ct_j * uz_i);
870
871	<	duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
872	<	duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
871	>	duduz_i += preSw * (ri3 * (uz_j - three * ct_j * rhat) - preRF2_*uz_j);
872	>	duduz_j += preSw * (ri3 * (uz_i - three * ct_i * rhat) - preRF2_*uz_i);
873
874	+	if (idat.excluded) {
875	+	indirect_vpair += - pref * preRF2_ * ct_ij;
876	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
877	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
878	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
879	+	}
880	+
881		} else {
882
883		if (i_is_SplitDipole) {
884		if (j_is_SplitDipole) {
885	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
885	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
886		} else {
887	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
887	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
888		}
889		ri = 1.0 / BigR;
890	<	scale = idat.rij * ri;
890	>	scale = (idat.rij) ri;
891		} else {
892		if (j_is_SplitDipole) {
893	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
893	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
894		ri = 1.0 / BigR;
895	<	scale = idat.rij * ri;
895	>	scale = (idat.rij) ri;
896		} else {
897		ri = riji;
898		scale = 1.0;
#	Line 723 \| Line 900 \| namespace OpenMD {
900		}
901		if (screeningMethod_ == DAMPED) {
902		// assemble damping variables
903	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
904	<	erfcVal = res.first;
905	<	derfcVal = res.second;
903	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
904	>	//erfcVal = res.first;
905	>	//derfcVal = res.second;
906	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
907	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
908		c1 = erfcVal * ri;
909		c2 = (-derfcVal + c1) * ri;
910		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 745 \| Line 924 \| namespace OpenMD {
924		preSwSc = preSw * scale;
925		c2ri = c2 * ri;
926		c3ri = c3 * ri;
927	<	c4rij = c4 * idat.rij;
927	>	c4rij = c4 * *(idat.rij) ;
928
929		// calculate the potential
930		pot_term = (ct_ij * c2ri - ctidotj * c3);
931		vterm = pref * pot_term;
932	<	idat.vpair += vterm;
933	<	epot += idat.sw * vterm;
932	>	vpair += vterm;
933	>	epot += (idat.sw) vterm;
934
935		// calculate derivatives for the forces and torques
936		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 770 \| Line 949 \| namespace OpenMD {
949		cy2 = cy_i * cy_i;
950		cz2 = cz_i * cz_i;
951
952	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
952	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
953
954		if (screeningMethod_ == DAMPED) {
955		// assemble the damping variables
956	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
957	<	erfcVal = res.first;
958	<	derfcVal = res.second;
956	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
957	>	//erfcVal = res.first;
958	>	//derfcVal = res.second;
959	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
960	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
961		c1 = erfcVal * riji;
962		c2 = (-derfcVal + c1) * riji;
963		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 789 \| Line 970 \| namespace OpenMD {
970		}
971
972		// precompute some variables for convenience
973	<	preSw = idat.sw * pref;
973	>	preSw = (idat.sw) pref;
974		c2ri = c2 * riji;
975		c3ri = c3 * riji;
976	<	c4rij = c4 * idat.rij;
977	<	rhatdot2 = 2.0 * rhat * c3;
976	>	c4rij = c4 * *(idat.rij) ;
977	>	rhatdot2 = two * rhat * c3;
978		rhatc4 = rhat * c4rij;
979
980		// calculate the potential
#	Line 802 \| Line 983 \| namespace OpenMD {
983		qzz_i * (cz2 * c3 - c2ri) );
984
985		vterm = pref * pot_term;
986	<	idat.vpair += vterm;
987	<	epot += idat.sw * vterm;
986	>	vpair += vterm;
987	>	epot += (idat.sw) vterm;
988
989		// calculate the derivatives for the forces and torques
990
991	<	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (2.0cx_iux_i + rhat)c3ri) +
992	<	qyy_i* (cy2rhatc4 - (2.0cy_iuy_i + rhat)c3ri) +
993	<	qzz_i* (cz2rhatc4 - (2.0cz_iuz_i + rhat)c3ri));
991	>	dVdr += -preSw * (qxx_i* (cx2rhatc4 - (twocx_iux_i + rhat)c3ri) +
992	>	qyy_i* (cy2rhatc4 - (twocy_iuy_i + rhat)c3ri) +
993	>	qzz_i* (cz2rhatc4 - (twocz_iuz_i + rhat)c3ri));
994
995		dudux_i += preSw * qxx_i * cx_i * rhatdot2;
996		duduy_i += preSw * qyy_i * cy_i * rhatdot2;
#	Line 817 \| Line 998 \| namespace OpenMD {
998		}
999		}
1000
820	–	idat.pot += epot;
821	–	idat.f1 += dVdr;
1001
1002	<	if (i_is_Dipole \|\| i_is_Quadrupole)
1003	<	idat.t1 -= cross(uz_i, duduz_i);
1004	<	if (i_is_Quadrupole) {
1005	<	idat.t1 -= cross(ux_i, dudux_i);
1006	<	idat.t1 -= cross(uy_i, duduy_i);
1007	<	}
1002	>	if (!idat.excluded) {
1003	>	*(idat.vpair) += vpair;
1004	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
1005	>	*(idat.f1) += dVdr;
1006	>
1007	>	if (i_is_Dipole \|\| i_is_Quadrupole)
1008	>	*(idat.t1) -= cross(uz_i, duduz_i);
1009	>	if (i_is_Quadrupole) {
1010	>	*(idat.t1) -= cross(ux_i, dudux_i);
1011	>	*(idat.t1) -= cross(uy_i, duduy_i);
1012	>	}
1013	>
1014	>	if (j_is_Dipole \|\| j_is_Quadrupole)
1015	>	*(idat.t2) -= cross(uz_j, duduz_j);
1016	>	if (j_is_Quadrupole) {
1017	>	*(idat.t2) -= cross(uz_j, dudux_j);
1018	>	*(idat.t2) -= cross(uz_j, duduy_j);
1019	>	}
1020
1021	<	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	<	}
1021	>	} else {
1022
1023	<	return;
1024	<	}
1023	>	// only accumulate the forces and torques resulting from the
1024	>	// indirect reaction field terms.
1025
1026	<	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
1027	<
1028	<	if (!initialized_) initialize();
843	<
844	<	ElectrostaticAtomData data1 = ElectrostaticMap[skdat.atype1];
845	<	ElectrostaticAtomData data2 = ElectrostaticMap[skdat.atype2];
846	<
847	<	// logicals
848	<
849	<	bool i_is_Charge = data1.is_Charge;
850	<	bool i_is_Dipole = data1.is_Dipole;
851	<
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:
1026	>	*(idat.vpair) += indirect_vpair;
1027	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
1028	>	*(idat.f1) += indirect_dVdr;
1029
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	–
1030		if (i_is_Dipole)
1031	<	skdat.t1 -= cross(uz_i, duduz_i);
1031	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
1032		if (j_is_Dipole)
1033	<	skdat.t2 -= cross(uz_j, duduz_j);
1033	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
1034		}
1035	<	}
1035	>
1036	>
1037	>	return;
1038	>	}
1039
1040	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1040	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1041		RealType mu1, preVal, chg1, self;
1042
1043		if (!initialized_) initialize();
1044	<
1045	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1044	>
1045	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1046
1047		// logicals
949	–
1048		bool i_is_Charge = data.is_Charge;
1049		bool i_is_Dipole = data.is_Dipole;
1050
1051	<	if (summationMethod_ == REACTION_FIELD) {
1051	>	if (summationMethod_ == esm_REACTION_FIELD) {
1052		if (i_is_Dipole) {
1053		mu1 = data.dipole_moment;
1054		preVal = pre22_ * preRF2_ * mu1 * mu1;
1055	<	scdat.pot -= 0.5 * preVal;
1055	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1056
1057		// The self-correction term adds into the reaction field vector
1058	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1058	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1059		Vector3d ei = preVal * uz_i;
1060
1061		// This looks very wrong. A vector crossed with itself is zero.
1062	<	scdat.t -= cross(uz_i, ei);
1062	>	*(sdat.t) -= cross(uz_i, ei);
1063		}
1064	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1064	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1065		if (i_is_Charge) {
1066	<	chg1 = data.charge;
1066	>	chg1 = data.fixedCharge;
1067		if (screeningMethod_ == DAMPED) {
1068	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1068	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1069		} else {
1070	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1070	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1071		}
1072	<	scdat.pot += self;
1072	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1073		}
1074		}
1075		}
1076	+
1077	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1078	+	// This seems to work moderately well as a default. There's no
1079	+	// inherent scale for 1/r interactions that we can standardize.
1080	+	// 12 angstroms seems to be a reasonably good guess for most
1081	+	// cases.
1082	+	return 12.0;
1083	+	}
1084		}

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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 1721 by gezelter, Thu May 24 14:17:42 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 1721 by gezelter, Thu May 24 14:17:42 2012 UTC