src/types/CharmmTorsionType.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
#include <cmath> 
#include "types/CharmmTorsionType.hpp"
#include "utils/NumericConstant.hpp"
namespace oopse {

  void CharmmTorsionType::calcForce(double cosPhi, double sinPhi, double& V, double& dVdPhi) {
    V = 0;
    dVdPhi = 0; 
    double phi = -std::atan2(sinPhi, cosPhi);
    
    std::vector<CharmmTorsionParameter>::iterator i;
    for (i = parameter_.begin(); i != parameter_.end(); ++i) {
      double kchi= i->kchi;
      int n = i->n;        
      double delta = i->delta;

      if (n == 0) {
        //if periodicity is equal to 0, use harmonic form
        double diff = phi - delta;

        if (diff < -NumericConstant::PI) {
          diff += NumericConstant::TWO_PI;
        } else if (diff > NumericConstant::PI) {
          diff -= NumericConstant::TWO_PI;
        }
            
        V += kchi * diff * diff;
        dVdPhi += 2.0 * kchi * diff;

      } else {
        //use normal cos form if periodicity is greater than 0
        V += kchi * (1 + std::cos(n * phi + delta));
        dVdPhi += -n * kchi * std::sin(n * phi + delta);
      }
    } 
  }

} //end namespace oopse
Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	3099 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41	tim	1937	#include <cmath>
42	gezelter	1930	#include "types/CharmmTorsionType.hpp"
43			#include "utils/NumericConstant.hpp"
44			namespace oopse {
45
46	gezelter	2204	void CharmmTorsionType::calcForce(double cosPhi, double sinPhi, double& V, double& dVdPhi) {
47	gezelter	1930	V = 0;
48			dVdPhi = 0;
49	tim	1937	double phi = -std::atan2(sinPhi, cosPhi);
50	gezelter	1930
51			std::vector<CharmmTorsionParameter>::iterator i;
52			for (i = parameter_.begin(); i != parameter_.end(); ++i) {
53	gezelter	2204	double kchi= i->kchi;
54			int n = i->n;
55			double delta = i->delta;
56	gezelter	1930
57	gezelter	2204	if (n == 0) {
58			//if periodicity is equal to 0, use harmonic form
59			double diff = phi - delta;
60	gezelter	1930
61	gezelter	2204	if (diff < -NumericConstant::PI) {
62			diff += NumericConstant::TWO_PI;
63			} else if (diff > NumericConstant::PI) {
64			diff -= NumericConstant::TWO_PI;
65			}
66	gezelter	1930
67	gezelter	2204	V += kchi * diff * diff;
68			dVdPhi += 2.0 * kchi * diff;
69	gezelter	1930
70	gezelter	2204	} else {
71			//use normal cos form if periodicity is greater than 0
72			V += kchi * (1 + std::cos(n * phi + delta));
73			dVdPhi += -n * kchi * std::sin(n * phi + delta);
74			}
75	gezelter	1930	}
76	gezelter	2204	}
77	gezelter	1930
78			} //end namespace oopse