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

Comparing:
trunk/src/primitives/Inversion.cpp (file contents), Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC vs.
branches/development/src/primitives/Inversion.cpp (file contents), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 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]  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/Inversion.hpp"
43	–	#include "fstream"
44
45	<	namespace oopse {
45	>	namespace OpenMD {
46
47		Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3,
48		Atom *atom4, InversionType *it) :
49		atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4),
50		inversionType_(it) { }
51
52	<	void Inversion::calcForce(RealType& angle) {
52	>	void Inversion::calcForce(RealType& angle, bool doParticlePot) {
53
54	<	// In OOPSE's version of an inversion, the central atom
54	>	// In OpenMD's version of an inversion, the central atom
55		// comes first.  However, to get the planarity in a typical cosine
56		// version of this potential (i.e. Amber-style), the central atom
57		// is treated as atom *3* in a standard torsion form:
#	Line 61 | Line 61 | namespace oopse {
61		Vector3d pos3 = atom1_->getPos();
62		Vector3d pos4 = atom4_->getPos();
63
64	–	/*std::ofstream myfile;
65	–	myfile.open("Inversion", std::ios::app);
66	–	myfile << atom1_->getType() << " - atom1; "
67	–	<< atom2_->getType() << " - atom2; "
68	–	<< atom3_->getType() << " - atom3; "
69	–	<< atom4_->getType() << " - atom4; "
70	–	<< std::endl;
71	–	*/
64		Vector3d r31 = pos1 - pos3;
65		Vector3d r23 = pos3 - pos2;
66		Vector3d r43 = pos3 - pos4;
#	Line 87 | Line 79 | namespace oopse {
79
80		//  Calculate the sin and cos
81		RealType cos_phi = dot(A, B) ;
82	<	if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0"
83	<	<< std::endl;}
92	<	if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0"
93	<	<< std::endl;}
94	<	//std::cout << "We actually use this inversion!!!!" << std::endl;
82	>	if (cos_phi > 1.0) cos_phi = 1.0;
83	>	if (cos_phi < -1.0) cos_phi = -1.0;
84
85		RealType dVdcosPhi;
97	–	//cos_phi = 2.0*cos_phi*cos_phi - 1.0;
86		inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
87		Vector3d f1 ;
88		Vector3d f2 ;
#	Line 107 | Line 95 | namespace oopse {
95		f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
96		f3 = dVdcosPhi * cross(dcosdB, r43);
97
98	<	// In OOPSE's version of an improper torsion, the central atom
98	>	// In OpenMD's version of an improper torsion, the central atom
99		// comes first.  However, to get the planarity in a typical cosine
100		// version of this potential (i.e. Amber-style), the central atom
101		// is treated as atom *3* in a standard torsion form:
102
103		//  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
104	<	//  OOPSE:   I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
104	>	//  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
105
106		// Confusing enough?  Good.
107
#	Line 122 | Line 110 | namespace oopse {
110		atom4_->addFrc(-f2);
111		atom3_->addFrc(-f3);
112
113	+	if (doParticlePot) {
114	+	atom1_->addParticlePot(potential_);
115	+	atom2_->addParticlePot(potential_);
116	+	atom3_->addParticlePot(potential_);
117	+	atom4_->addParticlePot(potential_);
118	+	}
119	+
120		angle = acos(cos_phi) /M_PI * 180.0;
121		}
122

Comparing:
trunk/src/primitives/Inversion.cpp (property svn:keywords), Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC vs.
branches/development/src/primitives/Inversion.cpp (property svn:keywords), Revision 1712 by gezelter, Sat May 19 13:30:21 2012 UTC

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