[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 1616 by gezelter, Tue Aug 30 15:45:35 2011 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).
40		*/
#	Line 47 \| Line 47
47		#include "utils/simError.h"
48		#include "types/NonBondedInteractionType.hpp"
49		#include "types/DirectionalAtomType.hpp"
50	+	#include "io/Globals.hpp"
51
51	–
52		namespace OpenMD {
53
54		Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
55	<	forceField_(NULL) {}
55	>	forceField_(NULL), info_(NULL),
56	>	haveCutoffRadius_(false),
57	>	haveDampingAlpha_(false),
58	>	haveDielectric_(false),
59	>	haveElectroSpline_(false)
60	>	{}
61
62		void Electrostatic::initialize() {
63	+
64	+	Globals* simParams_ = info_->getSimParams();
65	+
66	+	summationMap_["HARD"] = esm_HARD;
67	+	summationMap_["NONE"] = esm_HARD;
68	+	summationMap_["SWITCHING_FUNCTION"] = esm_SWITCHING_FUNCTION;
69	+	summationMap_["SHIFTED_POTENTIAL"] = esm_SHIFTED_POTENTIAL;
70	+	summationMap_["SHIFTED_FORCE"] = esm_SHIFTED_FORCE;
71	+	summationMap_["REACTION_FIELD"] = esm_REACTION_FIELD;
72	+	summationMap_["EWALD_FULL"] = esm_EWALD_FULL;
73	+	summationMap_["EWALD_PME"] = esm_EWALD_PME;
74	+	summationMap_["EWALD_SPME"] = esm_EWALD_SPME;
75	+	screeningMap_["DAMPED"] = DAMPED;
76	+	screeningMap_["UNDAMPED"] = UNDAMPED;
77	+
78		// these prefactors convert the multipole interactions into kcal / mol
79		// all were computed assuming distances are measured in angstroms
80		// Charge-Charge, assuming charges are measured in electrons
#	Line 79 \| Line 99 \| namespace OpenMD {
99
100		// variables to handle different summation methods for long-range
101		// electrostatics:
102	<	summationMethod_ = NONE;
102	>	summationMethod_ = esm_HARD;
103		screeningMethod_ = UNDAMPED;
104		dielectric_ = 1.0;
105		one_third_ = 1.0 / 3.0;
86	–	haveDefaultCutoff_ = false;
87	–	haveDampingAlpha_ = false;
88	–	haveDielectric_ = false;
89	–	haveElectroSpline_ = false;
106
107	+	// check the summation method:
108	+	if (simParams_->haveElectrostaticSummationMethod()) {
109	+	string myMethod = simParams_->getElectrostaticSummationMethod();
110	+	toUpper(myMethod);
111	+	map<string, ElectrostaticSummationMethod>::iterator i;
112	+	i = summationMap_.find(myMethod);
113	+	if ( i != summationMap_.end() ) {
114	+	summationMethod_ = (*i).second;
115	+	} else {
116	+	// throw error
117	+	sprintf( painCave.errMsg,
118	+	"Electrostatic::initialize: Unknown electrostaticSummationMethod.\n"
119	+	"\t(Input file specified %s .)\n"
120	+	"\telectrostaticSummationMethod must be one of: \"hard\",\n"
121	+	"\t\"shifted_potential\", \"shifted_force\", or \n"
122	+	"\t\"reaction_field\".\n", myMethod.c_str() );
123	+	painCave.isFatal = 1;
124	+	simError();
125	+	}
126	+	} else {
127	+	// set ElectrostaticSummationMethod to the cutoffMethod:
128	+	if (simParams_->haveCutoffMethod()){
129	+	string myMethod = simParams_->getCutoffMethod();
130	+	toUpper(myMethod);
131	+	map<string, ElectrostaticSummationMethod>::iterator i;
132	+	i = summationMap_.find(myMethod);
133	+	if ( i != summationMap_.end() ) {
134	+	summationMethod_ = (*i).second;
135	+	}
136	+	}
137	+	}
138	+
139	+	if (summationMethod_ == esm_REACTION_FIELD) {
140	+	if (!simParams_->haveDielectric()) {
141	+	// throw warning
142	+	sprintf( painCave.errMsg,
143	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
144	+	"\tA default value of %f will be used for the dielectric.\n", dielectric_);
145	+	painCave.isFatal = 0;
146	+	painCave.severity = OPENMD_INFO;
147	+	simError();
148	+	} else {
149	+	dielectric_ = simParams_->getDielectric();
150	+	}
151	+	haveDielectric_ = true;
152	+	}
153	+
154	+	if (simParams_->haveElectrostaticScreeningMethod()) {
155	+	string myScreen = simParams_->getElectrostaticScreeningMethod();
156	+	toUpper(myScreen);
157	+	map<string, ElectrostaticScreeningMethod>::iterator i;
158	+	i = screeningMap_.find(myScreen);
159	+	if ( i != screeningMap_.end()) {
160	+	screeningMethod_ = (*i).second;
161	+	} else {
162	+	sprintf( painCave.errMsg,
163	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
164	+	"\t(Input file specified %s .)\n"
165	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
166	+	"or \"damped\".\n", myScreen.c_str() );
167	+	painCave.isFatal = 1;
168	+	simError();
169	+	}
170	+	}
171	+
172	+	// check to make sure a cutoff value has been set:
173	+	if (!haveCutoffRadius_) {
174	+	sprintf( painCave.errMsg, "Electrostatic::initialize has no Default "
175	+	"Cutoff value!\n");
176	+	painCave.severity = OPENMD_ERROR;
177	+	painCave.isFatal = 1;
178	+	simError();
179	+	}
180	+
181	+	if (screeningMethod_ == DAMPED) {
182	+	if (!simParams_->haveDampingAlpha()) {
183	+	// first set a cutoff dependent alpha value
184	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
185	+	dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
186	+	if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
187	+
188	+	// throw warning
189	+	sprintf( painCave.errMsg,
190	+	"Electrostatic::initialize: dampingAlpha was not specified in the input file.\n"
191	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n",
192	+	dampingAlpha_, cutoffRadius_);
193	+	painCave.severity = OPENMD_INFO;
194	+	painCave.isFatal = 0;
195	+	simError();
196	+	} else {
197	+	dampingAlpha_ = simParams_->getDampingAlpha();
198	+	}
199	+	haveDampingAlpha_ = true;
200	+	}
201	+
202		// find all of the Electrostatic atom Types:
203		ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
204		ForceField::AtomTypeContainer::MapTypeIterator i;
205		AtomType* at;
206	<
206	>
207		for (at = atomTypes->beginType(i); at != NULL;
208		at = atomTypes->nextType(i)) {
209
#	Line 100 \| Line 211 \| namespace OpenMD {
211		addType(at);
212		}
213
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	–	}
214
215	<	defaultCutoff2_ = defaultCutoff_ * defaultCutoff_;
216	<	rcuti_ = 1.0 / defaultCutoff_;
215	>	cutoffRadius2_ = cutoffRadius_ * cutoffRadius_;
216	>	rcuti_ = 1.0 / cutoffRadius_;
217		rcuti2_ = rcuti_ * rcuti_;
218		rcuti3_ = rcuti2_ * rcuti_;
219		rcuti4_ = rcuti2_ * rcuti2_;
220
221		if (screeningMethod_ == DAMPED) {
222	<	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	<
222	>
223		alpha2_ = dampingAlpha_ * dampingAlpha_;
224		alpha4_ = alpha2_ * alpha2_;
225		alpha6_ = alpha4_ * alpha2_;
226		alpha8_ = alpha4_ * alpha4_;
227
228	<	constEXP_ = exp(-alpha2_ * defaultCutoff2_);
228	>	constEXP_ = exp(-alpha2_ * cutoffRadius2_);
229		invRootPi_ = 0.56418958354775628695;
230		alphaPi_ = 2.0 * dampingAlpha_ * invRootPi_;
231
232	<	c1c_ = erfc(dampingAlpha_ * defaultCutoff_) * rcuti_;
232	>	c1c_ = erfc(dampingAlpha_ * cutoffRadius_) * rcuti_;
233		c2c_ = alphaPi_ * constEXP_ * rcuti_ + c1c_ * rcuti_;
234		c3c_ = 2.0 * alphaPi_ * alpha2_ + 3.0 * c2c_ * rcuti_;
235		c4c_ = 4.0 * alphaPi_ * alpha4_ + 5.0 * c3c_ * rcuti2_;
#	Line 148 \| Line 244 \| namespace OpenMD {
244		c6c_ = 9.0 * c5c_ * rcuti2_;
245		}
246
247	<	if (summationMethod_ == REACTION_FIELD) {
248	<	if (haveDielectric_) {
249	<	preRF_ = (dielectric_ - 1.0) /
250	<	((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	<	}
247	>	if (summationMethod_ == esm_REACTION_FIELD) {
248	>	preRF_ = (dielectric_ - 1.0) /
249	>	((2.0 * dielectric_ + 1.0) * cutoffRadius2_ * cutoffRadius_);
250	>	preRF2_ = 2.0 * preRF_;
251		}
252	<
253	<	RealType dx = defaultCutoff_ / RealType(np_ - 1);
252	>
253	>	// Add a 2 angstrom safety window to deal with cutoffGroups that
254	>	// have charged atoms longer than the cutoffRadius away from each
255	>	// other. Splining may not be the best choice here. Direct calls
256	>	// to erfc might be preferrable.
257	>
258	>	RealType dx = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
259		RealType rval;
260		vector<RealType> rvals;
261		vector<RealType> yvals;
#	Line 283 \| Line 376 \| namespace OpenMD {
376		simError();
377		}
378
379	+	// Quadrupoles in OpenMD are set as the diagonal elements
380	+	// of the diagonalized traceless quadrupole moment tensor.
381	+	// The column vectors of the unitary matrix that diagonalizes
382	+	// the quadrupole moment tensor become the eFrame (or the
383	+	// electrostatic version of the body-fixed frame.
384	+
385		Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data);
386		if (v3dData == NULL) {
387		sprintf( painCave.errMsg,
#	Line 315 \| Line 414 \| namespace OpenMD {
414		return;
415		}
416
417	<	void Electrostatic::setElectrostaticCutoffRadius( RealType theECR,
418	<	RealType theRSW ) {
419	<	defaultCutoff_ = theECR;
420	<	rrf_ = defaultCutoff_;
322	<	rt_ = theRSW;
323	<	haveDefaultCutoff_ = true;
417	>	void Electrostatic::setCutoffRadius( RealType rCut ) {
418	>	cutoffRadius_ = rCut;
419	>	rrf_ = cutoffRadius_;
420	>	haveCutoffRadius_ = true;
421		}
422	+
423	+	void Electrostatic::setSwitchingRadius( RealType rSwitch ) {
424	+	rt_ = rSwitch;
425	+	}
426		void Electrostatic::setElectrostaticSummationMethod( ElectrostaticSummationMethod esm ) {
427		summationMethod_ = esm;
428		}
#	Line 337 \| Line 438 \| namespace OpenMD {
438		haveDielectric_ = true;
439		}
440
441	<	void Electrostatic::calcForce(InteractionData idat) {
441	>	void Electrostatic::calcForce(InteractionData &idat) {
442
443		// utility variables. Should clean these up and use the Vector3d and
444		// Mat3x3d to replace as many as we can in future versions:
#	Line 351 \| Line 452 \| namespace OpenMD {
452		RealType ct_i, ct_j, ct_ij, a1;
453		RealType riji, ri, ri2, ri3, ri4;
454		RealType pref, vterm, epot, dudr;
455	+	RealType vpair(0.0);
456		RealType scale, sc2;
457		RealType pot_term, preVal, rfVal;
458		RealType c2ri, c3ri, c4rij, cti3, ctj3, ctidotj;
459		RealType preSw, preSwSc;
460		RealType c1, c2, c3, c4;
461	<	RealType erfcVal, derfcVal;
461	>	RealType erfcVal(1.0), derfcVal(0.0);
462		RealType BigR;
463
464		Vector3d Q_i, Q_j;
#	Line 367 \| Line 469 \| namespace OpenMD {
469		Vector3d rhatdot2, rhatc4;
470		Vector3d dVdr;
471
472	+	// variables for indirect (reaction field) interactions for excluded pairs:
473	+	RealType indirect_Pot(0.0);
474	+	RealType indirect_vpair(0.0);
475	+	Vector3d indirect_dVdr(V3Zero);
476	+	Vector3d indirect_duduz_i(V3Zero), indirect_duduz_j(V3Zero);
477	+
478		pair<RealType, RealType> res;
479
480		if (!initialized_) initialize();
481
482	<	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atype1];
483	<	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atype2];
482	>	ElectrostaticAtomData data1 = ElectrostaticMap[idat.atypes.first];
483	>	ElectrostaticAtomData data2 = ElectrostaticMap[idat.atypes.second];
484
485		// some variables we'll need independent of electrostatic type:
486
487	<	riji = 1.0 / idat.rij;
488	<	Vector3d rhat = idat.d * riji;
487	>	riji = 1.0 / *(idat.rij) ;
488	>	Vector3d rhat = (idat.d) riji;
489
490		// logicals
491
#	Line 391 \| Line 499 \| namespace OpenMD {
499		bool j_is_SplitDipole = data2.is_SplitDipole;
500		bool j_is_Quadrupole = data2.is_Quadrupole;
501
502	<	if (i_is_Charge)
502	>	if (i_is_Charge) {
503		q_i = data1.charge;
504	+	if (idat.excluded) {
505	+	*(idat.skippedCharge2) += q_i;
506	+	}
507	+	}
508
509		if (i_is_Dipole) {
510		mu_i = data1.dipole_moment;
511	<	uz_i = idat.eFrame1.getColumn(2);
511	>	uz_i = idat.eFrame1->getColumn(2);
512
513		ct_i = dot(uz_i, rhat);
514
#	Line 412 \| Line 524 \| namespace OpenMD {
524		qyy_i = Q_i.y();
525		qzz_i = Q_i.z();
526
527	<	ux_i = idat.eFrame1.getColumn(0);
528	<	uy_i = idat.eFrame1.getColumn(1);
529	<	uz_i = idat.eFrame1.getColumn(2);
527	>	ux_i = idat.eFrame1->getColumn(0);
528	>	uy_i = idat.eFrame1->getColumn(1);
529	>	uz_i = idat.eFrame1->getColumn(2);
530
531		cx_i = dot(ux_i, rhat);
532		cy_i = dot(uy_i, rhat);
#	Line 425 \| Line 537 \| namespace OpenMD {
537		duduz_i = V3Zero;
538		}
539
540	<	if (j_is_Charge)
540	>	if (j_is_Charge) {
541		q_j = data2.charge;
542	+	if (idat.excluded) {
543	+	*(idat.skippedCharge1) += q_j;
544	+	}
545	+	}
546
547	+
548		if (j_is_Dipole) {
549		mu_j = data2.dipole_moment;
550	<	uz_j = idat.eFrame2.getColumn(2);
550	>	uz_j = idat.eFrame2->getColumn(2);
551
552		ct_j = dot(uz_j, rhat);
553
#	Line 446 \| Line 563 \| namespace OpenMD {
563		qyy_j = Q_j.y();
564		qzz_j = Q_j.z();
565
566	<	ux_j = idat.eFrame2.getColumn(0);
567	<	uy_j = idat.eFrame2.getColumn(1);
568	<	uz_j = idat.eFrame2.getColumn(2);
566	>	ux_j = idat.eFrame2->getColumn(0);
567	>	uy_j = idat.eFrame2->getColumn(1);
568	>	uz_j = idat.eFrame2->getColumn(2);
569
570		cx_j = dot(ux_j, rhat);
571		cy_j = dot(uy_j, rhat);
#	Line 467 \| Line 584 \| namespace OpenMD {
584		if (j_is_Charge) {
585		if (screeningMethod_ == DAMPED) {
586		// assemble the damping variables
587	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
588	<	erfcVal = res.first;
589	<	derfcVal = res.second;
587	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
588	>	//erfcVal = res.first;
589	>	//derfcVal = res.second;
590	>
591	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
592	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
593	>
594		c1 = erfcVal * riji;
595		c2 = (-derfcVal + c1) * riji;
596		} else {
#	Line 477 \| Line 598 \| namespace OpenMD {
598		c2 = c1 * riji;
599		}
600
601	<	preVal = idat.electroMult * pre11_ * q_i * q_j;
601	>	preVal = (idat.electroMult) pre11_ * q_i * q_j;
602
603	<	if (summationMethod_ == SHIFTED_POTENTIAL) {
603	>	if (summationMethod_ == esm_SHIFTED_POTENTIAL) {
604		vterm = preVal * (c1 - c1c_);
605	<	dudr = -idat.sw * preVal * c2;
605	>	dudr = - (idat.sw) preVal * c2;
606
607	<	} else if (summationMethod_ == SHIFTED_FORCE) {
608	<	vterm = preVal * ( c1 - c1c_ + c2c_*(idat.rij - defaultCutoff_) );
609	<	dudr = idat.sw * preVal * (c2c_ - c2);
607	>	} else if (summationMethod_ == esm_SHIFTED_FORCE) {
608	>	vterm = preVal * ( c1 - c1c_ + c2c_( (idat.rij) - cutoffRadius_) );
609	>	dudr = (idat.sw) preVal * (c2c_ - c2);
610
611	<	} else if (summationMethod_ == REACTION_FIELD) {
612	<	rfVal = idat.electroMult * preRF_ * idat.rij * idat.rij;
611	>	} else if (summationMethod_ == esm_REACTION_FIELD) {
612	>	rfVal = preRF_ * (idat.rij) *(idat.rij);
613	>
614		vterm = preVal * ( riji + rfVal );
615	<	dudr = idat.sw * preVal * ( 2.0 * rfVal - riji ) * riji;
615	>	dudr = (idat.sw) preVal * ( 2.0 * rfVal - riji ) * riji;
616	>
617	>	// if this is an excluded pair, there are still indirect
618	>	// interactions via the reaction field we must worry about:
619
620	+	if (idat.excluded) {
621	+	indirect_vpair += preVal * rfVal;
622	+	indirect_Pot += (idat.sw) preVal * rfVal;
623	+	indirect_dVdr += (idat.sw) preVal * 2.0 * rfVal * riji * rhat;
624	+	}
625	+
626		} else {
496	–	vterm = preVal * riji * erfcVal;
627
628	<	dudr = - idat.sw * preVal * c2;
628	>	vterm = preVal * riji * erfcVal;
629	>	dudr = - (idat.sw) preVal * c2;
630
631		}
501	–
502	–	idat.vpair += vterm;
503	–	epot += idat.sw * vterm;
632
633	<	dVdr += dudr * rhat;
633	>	vpair += vterm;
634	>	epot += (idat.sw) vterm;
635	>	dVdr += dudr * rhat;
636		}
637
638		if (j_is_Dipole) {
639		// pref is used by all the possible methods
640	<	pref = idat.electroMult * pre12_ * q_i * mu_j;
641	<	preSw = idat.sw * pref;
640	>	pref = (idat.electroMult) pre12_ * q_i * mu_j;
641	>	preSw = (idat.sw) pref;
642
643	<	if (summationMethod_ == REACTION_FIELD) {
643	>	if (summationMethod_ == esm_REACTION_FIELD) {
644		ri2 = riji * riji;
645		ri3 = ri2 * riji;
646
647	<	vterm = - pref * ct_j * ( ri2 - preRF2_ * idat.rij );
648	<	idat.vpair += vterm;
649	<	epot += idat.sw * vterm;
647	>	vterm = - pref * ct_j * ( ri2 - preRF2_ * *(idat.rij) );
648	>	vpair += vterm;
649	>	epot += (idat.sw) vterm;
650
651		dVdr += -preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
652	<	duduz_j += -preSw * rhat * (ri2 - preRF2_ * idat.rij);
652	>	duduz_j += -preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
653
654	+	// Even if we excluded this pair from direct interactions,
655	+	// we still have the reaction-field-mediated charge-dipole
656	+	// interaction:
657	+
658	+	if (idat.excluded) {
659	+	indirect_vpair += pref * ct_j * preRF2_ * *(idat.rij);
660	+	indirect_Pot += preSw * ct_j * preRF2_ * *(idat.rij);
661	+	indirect_dVdr += preSw * preRF2_ * uz_j;
662	+	indirect_duduz_j += preSw * rhat * preRF2_ * *(idat.rij);
663	+	}
664	+
665		} else {
666		// determine the inverse r used if we have split dipoles
667		if (j_is_SplitDipole) {
668	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
668	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
669		ri = 1.0 / BigR;
670	<	scale = idat.rij * ri;
670	>	scale = (idat.rij) ri;
671		} else {
672		ri = riji;
673		scale = 1.0;
#	Line 536 \| Line 677 \| namespace OpenMD {
677
678		if (screeningMethod_ == DAMPED) {
679		// assemble the damping variables
680	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
681	<	erfcVal = res.first;
682	<	derfcVal = res.second;
680	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
681	>	//erfcVal = res.first;
682	>	//derfcVal = res.second;
683	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
684	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
685		c1 = erfcVal * ri;
686		c2 = (-derfcVal + c1) * ri;
687		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 553 \| Line 696 \| namespace OpenMD {
696		// calculate the potential
697		pot_term = scale * c2;
698		vterm = -pref * ct_j * pot_term;
699	<	idat.vpair += vterm;
700	<	epot += idat.sw * vterm;
699	>	vpair += vterm;
700	>	epot += (idat.sw) vterm;
701
702		// calculate derivatives for forces and torques
703
#	Line 569 \| Line 712 \| namespace OpenMD {
712		cx2 = cx_j * cx_j;
713		cy2 = cy_j * cy_j;
714		cz2 = cz_j * cz_j;
715	<	pref = idat.electroMult * pre14_ * q_i * one_third_;
715	>	pref = (idat.electroMult) pre14_ * q_i * one_third_;
716
717		if (screeningMethod_ == DAMPED) {
718		// assemble the damping variables
719	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
720	<	erfcVal = res.first;
721	<	derfcVal = res.second;
719	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
720	>	//erfcVal = res.first;
721	>	//derfcVal = res.second;
722	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
723	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
724		c1 = erfcVal * riji;
725		c2 = (-derfcVal + c1) * riji;
726		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 588 \| Line 733 \| namespace OpenMD {
733		}
734
735		// precompute variables for convenience
736	<	preSw = idat.sw * pref;
736	>	preSw = (idat.sw) pref;
737		c2ri = c2 * riji;
738		c3ri = c3 * riji;
739	<	c4rij = c4 * idat.rij;
739	>	c4rij = c4 * *(idat.rij) ;
740		rhatdot2 = 2.0 * rhat * c3;
741		rhatc4 = rhat * c4rij;
742
#	Line 600 \| Line 745 \| namespace OpenMD {
745		qyy_j * (cy2*c3 - c2ri) +
746		qzz_j * (cz2*c3 - c2ri) );
747		vterm = pref * pot_term;
748	<	idat.vpair += vterm;
749	<	epot += idat.sw * vterm;
748	>	vpair += vterm;
749	>	epot += (idat.sw) vterm;
750
751		// calculate derivatives for the forces and torques
752
#	Line 619 \| Line 764 \| namespace OpenMD {
764
765		if (j_is_Charge) {
766		// variables used by all the methods
767	<	pref = idat.electroMult * pre12_ * q_j * mu_i;
768	<	preSw = idat.sw * pref;
767	>	pref = (idat.electroMult) pre12_ * q_j * mu_i;
768	>	preSw = (idat.sw) pref;
769
770	<	if (summationMethod_ == REACTION_FIELD) {
770	>	if (summationMethod_ == esm_REACTION_FIELD) {
771
772		ri2 = riji * riji;
773		ri3 = ri2 * riji;
774
775	<	vterm = pref * ct_i * ( ri2 - preRF2_ * idat.rij );
776	<	idat.vpair += vterm;
777	<	epot += idat.sw * vterm;
775	>	vterm = pref * ct_i * ( ri2 - preRF2_ * *(idat.rij) );
776	>	vpair += vterm;
777	>	epot += (idat.sw) vterm;
778
779		dVdr += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_ * uz_i);
780
781	<	duduz_i += preSw * rhat * (ri2 - preRF2_ * idat.rij);
781	>	duduz_i += preSw * rhat * (ri2 - preRF2_ * *(idat.rij) );
782	>
783	>	// Even if we excluded this pair from direct interactions,
784	>	// we still have the reaction-field-mediated charge-dipole
785	>	// interaction:
786	>
787	>	if (idat.excluded) {
788	>	indirect_vpair += -pref * ct_i * preRF2_ * *(idat.rij);
789	>	indirect_Pot += -preSw * ct_i * preRF2_ * *(idat.rij);
790	>	indirect_dVdr += -preSw * preRF2_ * uz_i;
791	>	indirect_duduz_i += -preSw * rhat * preRF2_ * *(idat.rij);
792	>	}
793
794		} else {
795
796		// determine inverse r if we are using split dipoles
797		if (i_is_SplitDipole) {
798	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
798	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
799		ri = 1.0 / BigR;
800	<	scale = idat.rij * ri;
800	>	scale = (idat.rij) ri;
801		} else {
802		ri = riji;
803		scale = 1.0;
#	Line 651 \| Line 807 \| namespace OpenMD {
807
808		if (screeningMethod_ == DAMPED) {
809		// assemble the damping variables
810	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
811	<	erfcVal = res.first;
812	<	derfcVal = res.second;
810	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
811	>	//erfcVal = res.first;
812	>	//derfcVal = res.second;
813	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
814	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
815		c1 = erfcVal * ri;
816		c2 = (-derfcVal + c1) * ri;
817		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 668 \| Line 826 \| namespace OpenMD {
826		// calculate the potential
827		pot_term = c2 * scale;
828		vterm = pref * ct_i * pot_term;
829	<	idat.vpair += vterm;
830	<	epot += idat.sw * vterm;
829	>	vpair += vterm;
830	>	epot += (idat.sw) vterm;
831
832		// calculate derivatives for the forces and torques
833		dVdr += preSw * (uz_i * c2ri - ct_i * rhat * sc2 * c3);
#	Line 681 \| Line 839 \| namespace OpenMD {
839		// variables used by all methods
840		ct_ij = dot(uz_i, uz_j);
841
842	<	pref = idat.electroMult * pre22_ * mu_i * mu_j;
843	<	preSw = idat.sw * pref;
842	>	pref = (idat.electroMult) pre22_ * mu_i * mu_j;
843	>	preSw = (idat.sw) pref;
844
845	<	if (summationMethod_ == REACTION_FIELD) {
845	>	if (summationMethod_ == esm_REACTION_FIELD) {
846		ri2 = riji * riji;
847		ri3 = ri2 * riji;
848		ri4 = ri2 * ri2;
849
850		vterm = pref * ( ri3 * (ct_ij - 3.0 * ct_i * ct_j) -
851		preRF2_ * ct_ij );
852	<	idat.vpair += vterm;
853	<	epot += idat.sw * vterm;
852	>	vpair += vterm;
853	>	epot += (idat.sw) vterm;
854
855		a1 = 5.0 * ct_i * ct_j - ct_ij;
856
#	Line 700 \| Line 858 \| namespace OpenMD {
858
859		duduz_i += preSw * (ri3 * (uz_j - 3.0 * ct_j * rhat) - preRF2_*uz_j);
860		duduz_j += preSw * (ri3 * (uz_i - 3.0 * ct_i * rhat) - preRF2_*uz_i);
861	+
862	+	if (idat.excluded) {
863	+	indirect_vpair += - pref * preRF2_ * ct_ij;
864	+	indirect_Pot += - preSw * preRF2_ * ct_ij;
865	+	indirect_duduz_i += -preSw * preRF2_ * uz_j;
866	+	indirect_duduz_j += -preSw * preRF2_ * uz_i;
867	+	}
868
869		} else {
870
871		if (i_is_SplitDipole) {
872		if (j_is_SplitDipole) {
873	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i + 0.25 * d_j * d_j);
873	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i + 0.25 * d_j * d_j);
874		} else {
875	<	BigR = sqrt(idat.r2 + 0.25 * d_i * d_i);
875	>	BigR = sqrt( (idat.r2) + 0.25 d_i * d_i);
876		}
877		ri = 1.0 / BigR;
878	<	scale = idat.rij * ri;
878	>	scale = (idat.rij) ri;
879		} else {
880		if (j_is_SplitDipole) {
881	<	BigR = sqrt(idat.r2 + 0.25 * d_j * d_j);
881	>	BigR = sqrt( (idat.r2) + 0.25 d_j * d_j);
882		ri = 1.0 / BigR;
883	<	scale = idat.rij * ri;
883	>	scale = (idat.rij) ri;
884		} else {
885		ri = riji;
886		scale = 1.0;
#	Line 723 \| Line 888 \| namespace OpenMD {
888		}
889		if (screeningMethod_ == DAMPED) {
890		// assemble damping variables
891	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
892	<	erfcVal = res.first;
893	<	derfcVal = res.second;
891	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
892	>	//erfcVal = res.first;
893	>	//derfcVal = res.second;
894	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
895	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
896		c1 = erfcVal * ri;
897		c2 = (-derfcVal + c1) * ri;
898		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * ri;
#	Line 745 \| Line 912 \| namespace OpenMD {
912		preSwSc = preSw * scale;
913		c2ri = c2 * ri;
914		c3ri = c3 * ri;
915	<	c4rij = c4 * idat.rij;
915	>	c4rij = c4 * *(idat.rij) ;
916
917		// calculate the potential
918		pot_term = (ct_ij * c2ri - ctidotj * c3);
919		vterm = pref * pot_term;
920	<	idat.vpair += vterm;
921	<	epot += idat.sw * vterm;
920	>	vpair += vterm;
921	>	epot += (idat.sw) vterm;
922
923		// calculate derivatives for the forces and torques
924		dVdr += preSwSc * ( ctidotj * rhat * c4rij -
#	Line 770 \| Line 937 \| namespace OpenMD {
937		cy2 = cy_i * cy_i;
938		cz2 = cz_i * cz_i;
939
940	<	pref = idat.electroMult * pre14_ * q_j * one_third_;
940	>	pref = (idat.electroMult) pre14_ * q_j * one_third_;
941
942		if (screeningMethod_ == DAMPED) {
943		// assemble the damping variables
944	<	res = erfcSpline_->getValueAndDerivativeAt(idat.rij);
945	<	erfcVal = res.first;
946	<	derfcVal = res.second;
944	>	//res = erfcSpline_->getValueAndDerivativeAt( *(idat.rij) );
945	>	//erfcVal = res.first;
946	>	//derfcVal = res.second;
947	>	erfcVal = erfc(dampingAlpha_ * *(idat.rij));
948	>	derfcVal = - alphaPi_ * exp(-alpha2_ * *(idat.r2));
949		c1 = erfcVal * riji;
950		c2 = (-derfcVal + c1) * riji;
951		c3 = -2.0 * derfcVal * alpha2_ + 3.0 * c2 * riji;
#	Line 789 \| Line 958 \| namespace OpenMD {
958		}
959
960		// precompute some variables for convenience
961	<	preSw = idat.sw * pref;
961	>	preSw = (idat.sw) pref;
962		c2ri = c2 * riji;
963		c3ri = c3 * riji;
964	<	c4rij = c4 * idat.rij;
964	>	c4rij = c4 * *(idat.rij) ;
965		rhatdot2 = 2.0 * rhat * c3;
966		rhatc4 = rhat * c4rij;
967
#	Line 802 \| Line 971 \| namespace OpenMD {
971		qzz_i * (cz2 * c3 - c2ri) );
972
973		vterm = pref * pot_term;
974	<	idat.vpair += vterm;
975	<	epot += idat.sw * vterm;
974	>	vpair += vterm;
975	>	epot += (idat.sw) vterm;
976
977		// calculate the derivatives for the forces and torques
978
#	Line 817 \| Line 986 \| namespace OpenMD {
986		}
987		}
988
820	–	idat.pot += epot;
821	–	idat.f1 += dVdr;
989
990	<	if (i_is_Dipole \|\| i_is_Quadrupole)
991	<	idat.t1 -= cross(uz_i, duduz_i);
992	<	if (i_is_Quadrupole) {
993	<	idat.t1 -= cross(ux_i, dudux_i);
994	<	idat.t1 -= cross(uy_i, duduy_i);
995	<	}
990	>	if (!idat.excluded) {
991	>	*(idat.vpair) += vpair;
992	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += epot;
993	>	*(idat.f1) += dVdr;
994	>
995	>	if (i_is_Dipole \|\| i_is_Quadrupole)
996	>	*(idat.t1) -= cross(uz_i, duduz_i);
997	>	if (i_is_Quadrupole) {
998	>	*(idat.t1) -= cross(ux_i, dudux_i);
999	>	*(idat.t1) -= cross(uy_i, duduy_i);
1000	>	}
1001	>
1002	>	if (j_is_Dipole \|\| j_is_Quadrupole)
1003	>	*(idat.t2) -= cross(uz_j, duduz_j);
1004	>	if (j_is_Quadrupole) {
1005	>	*(idat.t2) -= cross(uz_j, dudux_j);
1006	>	*(idat.t2) -= cross(uz_j, duduy_j);
1007	>	}
1008	>
1009	>	} else {
1010	>
1011	>	// only accumulate the forces and torques resulting from the
1012	>	// indirect reaction field terms.
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);
1014	>	*(idat.vpair) += indirect_vpair;
1015	>	(*(idat.pot))[ELECTROSTATIC_FAMILY] += indirect_Pot;
1016	>	*(idat.f1) += indirect_dVdr;
1017	>
1018	>	if (i_is_Dipole)
1019	>	*(idat.t1) -= cross(uz_i, indirect_duduz_i);
1020	>	if (j_is_Dipole)
1021	>	*(idat.t2) -= cross(uz_j, indirect_duduz_j);
1022		}
1023
1024	+
1025		return;
1026		}
839	–
840	–	void Electrostatic::calcSkipCorrection(SkipCorrectionData skdat) {
841	–
842	–	if (!initialized_) initialize();
1027
1028	<	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:
880	<
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	<
934	<	if (i_is_Dipole)
935	<	skdat.t1 -= cross(uz_i, duduz_i);
936	<	if (j_is_Dipole)
937	<	skdat.t2 -= cross(uz_j, duduz_j);
938	<	}
939	<	}
940	<
941	<	void Electrostatic::calcSelfCorrection(SelfCorrectionData scdat) {
1028	>	void Electrostatic::calcSelfCorrection(SelfData &sdat) {
1029		RealType mu1, preVal, chg1, self;
1030
1031		if (!initialized_) initialize();
1032	<
1033	<	ElectrostaticAtomData data = ElectrostaticMap[scdat.atype];
1032	>
1033	>	ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1034
1035		// logicals
949	–
1036		bool i_is_Charge = data.is_Charge;
1037		bool i_is_Dipole = data.is_Dipole;
1038
1039	<	if (summationMethod_ == REACTION_FIELD) {
1039	>	if (summationMethod_ == esm_REACTION_FIELD) {
1040		if (i_is_Dipole) {
1041		mu1 = data.dipole_moment;
1042		preVal = pre22_ * preRF2_ * mu1 * mu1;
1043	<	scdat.pot -= 0.5 * preVal;
1043	>	((sdat.pot))[ELECTROSTATIC_FAMILY] -= 0.5 preVal;
1044
1045		// The self-correction term adds into the reaction field vector
1046	<	Vector3d uz_i = scdat.eFrame.getColumn(2);
1046	>	Vector3d uz_i = sdat.eFrame->getColumn(2);
1047		Vector3d ei = preVal * uz_i;
1048
1049		// This looks very wrong. A vector crossed with itself is zero.
1050	<	scdat.t -= cross(uz_i, ei);
1050	>	*(sdat.t) -= cross(uz_i, ei);
1051		}
1052	<	} else if (summationMethod_ == SHIFTED_FORCE \|\| summationMethod_ == SHIFTED_POTENTIAL) {
1052	>	} else if (summationMethod_ == esm_SHIFTED_FORCE \|\| summationMethod_ == esm_SHIFTED_POTENTIAL) {
1053		if (i_is_Charge) {
1054		chg1 = data.charge;
1055		if (screeningMethod_ == DAMPED) {
1056	<	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1056	>	self = - 0.5 * (c1c_ + alphaPi_) * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1057		} else {
1058	<	self = - 0.5 * rcuti_ * chg1 * (chg1 + scdat.skippedCharge) * pre11_;
1058	>	self = - 0.5 * rcuti_ * chg1 * (chg1 + (sdat.skippedCharge)) pre11_;
1059		}
1060	<	scdat.pot += self;
1060	>	(*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1061		}
1062		}
1063		}
1064	+
1065	+	RealType Electrostatic::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
1066	+	// This seems to work moderately well as a default. There's no
1067	+	// inherent scale for 1/r interactions that we can standardize.
1068	+	// 12 angstroms seems to be a reasonably good guess for most
1069	+	// cases.
1070	+	return 12.0;
1071	+	}
1072		}

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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 1616 by gezelter, Tue Aug 30 15:45:35 2011 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 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC