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Comparing trunk/src/primitives/Inversion.cpp (file contents):
Revision 1305 by skuang, Thu Oct 16 18:17:41 2008 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
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).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "primitives/Inversion.hpp"
43
44	<	namespace oopse {
44	>	namespace OpenMD {
45
46		Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3,
47		Atom *atom4, InversionType *it) :
#	Line 50 | Line 50 | namespace oopse {
50
51		void Inversion::calcForce(RealType& angle) {
52
53	<	// In OOPSE's version of an inversion, the central atom
53	>	// In OpenMD's version of an inversion, the central atom
54		// comes first.  However, to get the planarity in a typical cosine
55		// version of this potential (i.e. Amber-style), the central atom
56		// is treated as atom *3* in a standard torsion form:
#	Line 60 | Line 60 | namespace oopse {
60		Vector3d pos3 = atom1_->getPos();
61		Vector3d pos4 = atom4_->getPos();
62
63	–	/*std::ofstream myfile;
64	–	myfile.open("Inversion", std::ios::app);
65	–	myfile << atom1_->getType() << " - atom1; "
66	–	<< atom2_->getType() << " - atom2; "
67	–	<< atom3_->getType() << " - atom3; "
68	–	<< atom4_->getType() << " - atom4; "
69	–	<< std::endl;
70	–	*/
63		Vector3d r31 = pos1 - pos3;
64		Vector3d r23 = pos3 - pos2;
65		Vector3d r43 = pos3 - pos4;
#	Line 86 | Line 78 | namespace oopse {
78
79		//  Calculate the sin and cos
80		RealType cos_phi = dot(A, B) ;
81	<	if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0"
82	<	<< std::endl;}
91	<	if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0"
92	<	<< std::endl;}
93	<	//std::cout << "We actually use this inversion!!!!" << std::endl;
81	>	if (cos_phi > 1.0) cos_phi = 1.0;
82	>	if (cos_phi < -1.0) cos_phi = -1.0;
83
84		RealType dVdcosPhi;
96	–	//cos_phi = 2.0*cos_phi*cos_phi - 1.0;
85		inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
86		Vector3d f1 ;
87		Vector3d f2 ;
#	Line 106 | Line 94 | namespace oopse {
94		f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
95		f3 = dVdcosPhi * cross(dcosdB, r43);
96
97	<	// In OOPSE's version of an improper torsion, the central atom
97	>	// In OpenMD's version of an improper torsion, the central atom
98		// comes first.  However, to get the planarity in a typical cosine
99		// version of this potential (i.e. Amber-style), the central atom
100		// is treated as atom *3* in a standard torsion form:
101
102		//  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
103	<	//  OOPSE:   I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
103	>	//  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
104
105		// Confusing enough?  Good.
106
#	Line 121 | Line 109 | namespace oopse {
109		atom4_->addFrc(-f2);
110		atom3_->addFrc(-f3);
111
112	+	atom1_->addParticlePot(potential_);
113	+	atom2_->addParticlePot(potential_);
114	+	atom3_->addParticlePot(potential_);
115	+	atom4_->addParticlePot(potential_);
116	+
117		angle = acos(cos_phi) /M_PI * 180.0;
118		}
119

Comparing trunk/src/primitives/Inversion.cpp (property svn:keywords):
Revision 1305 by skuang, Thu Oct 16 18:17:41 2008 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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