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root/OpenMD/branches/development/src/primitives/Torsion.cpp

Comparing:
trunk/src/primitives/Torsion.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/primitives/Torsion.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 36 | Line 36
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).
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 "primitives/Torsion.hpp"
#	Line 63 | Line 64 | namespace OpenMD {
64		RealType rA = A.length();
65		Vector3d B = cross(r32, r43);
66		RealType rB = B.length();
66	–	Vector3d C = cross(r32, A);
67	–	RealType rC = C.length();
67
68	+	/*
69	+	If either of the two cross product vectors is tiny, that means
70	+	the three atoms involved are colinear, and the torsion angle is
71	+	going to be undefined.  The easiest check for this problem is
72	+	to use the product of the two lengths.
73	+	*/
74	+	if (rA * rB < OpenMD::epsilon) return;
75	+
76		A.normalize();
77	<	B.normalize();
71	<	C.normalize();
77	>	B.normalize();
78
79		//  Calculate the sin and cos
80		RealType cos_phi = dot(A, B) ;
81		if (cos_phi > 1.0) cos_phi = 1.0;
82		if (cos_phi < -1.0) cos_phi = -1.0;
83	<
83	>
84		RealType dVdcosPhi;
85		torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
86		Vector3d f1 ;
87		Vector3d f2 ;
88		Vector3d f3 ;
89	<
89	>
90		Vector3d dcosdA = (cos_phi * A - B) /rA;
91		Vector3d dcosdB = (cos_phi * B - A) /rB;
92	<
92	>
93		f1 = dVdcosPhi * cross(r32, dcosdA);
94		f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
95		f3 = dVdcosPhi * cross(dcosdB, r32);
#	Line 92 | Line 98 | namespace OpenMD {
98		atom2_->addFrc(f2 - f1);
99		atom3_->addFrc(f3 - f2);
100		atom4_->addFrc(-f3);
101	<
101	>
102		atom1_->addParticlePot(potential_);
103		atom2_->addParticlePot(potential_);
104		atom3_->addParticlePot(potential_);
105		atom4_->addParticlePot(potential_);
106	<
107	<	angle = acos(cos_phi) /M_PI * 180.0;
108	<	}
103	<
106	>
107	>	angle = acos(cos_phi) /M_PI * 180.0;
108	>	}
109		}

Comparing:
trunk/src/primitives/Torsion.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/primitives/Torsion.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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