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root/OpenMD/trunk/src/primitives/Inversion.cpp

Comparing trunk/src/primitives/Inversion.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1890 by gezelter, Tue Jun 18 21:06:25 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
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 "config.h"
44	+	#include <cmath>
45	+
46		#include "primitives/Inversion.hpp"
47
48		namespace OpenMD {
#	Line 46 | Line 50 | namespace OpenMD {
50		Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3,
51		Atom *atom4, InversionType *it) :
52		atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4),
53	<	inversionType_(it) { }
53	>	inversionType_(it) {
54	>	inversionKey_ = inversionType_->getKey();
55	>	}
56
57	<	void Inversion::calcForce(RealType& angle) {
57	>	void Inversion::calcForce(RealType& angle, bool doParticlePot) {
58
59		// In OpenMD's version of an inversion, the central atom
60		// comes first.  However, to get the planarity in a typical cosine
#	Line 82 | Line 88 | namespace OpenMD {
88		if (cos_phi < -1.0) cos_phi = -1.0;
89
90		RealType dVdcosPhi;
91	<	inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
91	>	switch (inversionKey_) {
92	>	case itCosAngle:
93	>	inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
94	>	break;
95	>	case itAngle:
96	>	RealType phi = acos(cos_phi);
97	>	RealType dVdPhi;
98	>	inversionType_->calcForce(phi, potential_, dVdPhi);
99	>	RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi);
100	>	if (fabs(sin_phi) < 1.0E-6) {
101	>	sin_phi = 1.0E-6;
102	>	}
103	>	dVdcosPhi = dVdPhi / sin_phi;
104	>	break;
105	>	}
106	>
107		Vector3d f1 ;
108		Vector3d f2 ;
109		Vector3d f3 ;
#	Line 109 | Line 130 | namespace OpenMD {
130		atom4_->addFrc(-f2);
131		atom3_->addFrc(-f3);
132
133	<	atom1_->addParticlePot(potential_);
134	<	atom2_->addParticlePot(potential_);
135	<	atom3_->addParticlePot(potential_);
136	<	atom4_->addParticlePot(potential_);
137	<
133	>	if (doParticlePot) {
134	>	atom1_->addParticlePot(potential_);
135	>	atom2_->addParticlePot(potential_);
136	>	atom3_->addParticlePot(potential_);
137	>	atom4_->addParticlePot(potential_);
138	>	}
139	>
140		angle = acos(cos_phi) /M_PI * 180.0;
141		}
142

Comparing trunk/src/primitives/Inversion.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1890 by gezelter, Tue Jun 18 21:06:25 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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