src/restraints/Restraints.hpp

/*
 * 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.
 */

#ifndef _RESTRAINTS_H_
#define _RESTRAINTS_H_

#include <stdlib.h>
#include <vector>
#include "primitives/Atom.hpp"
#include "brains/SimInfo.hpp"
#include "io/RestReader.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"

namespace oopse {
  
  class Restraints{
    
  public:
    Restraints(SimInfo * info, double lambdaVal, double lambdaExp);
    ~Restraints();
    
    void Calc_rVal(Vector3d &position, double refPosition[3]);
    void Calc_body_thetaVal(RotMat3x3d &matrix, double refUnit[3]);
    void Calc_body_omegaVal(double zAngle);
    double Calc_Restraint_Forces();
    double getVharm() { return harmPotent; }
    
  private:
    SimInfo * info_;
    RestReader* restRead_;
    
    char moleculeName[15];
    
    int i, j;
    
    double scaleLam;
    double delRx, delRy, delRz;
    double theta, omega;
    double vProj0[3];
    double vProjDist;
    double uTx, uTy, uTz, vTx, vTy, vTz;
    double ub0x, ub0y, ub0z, vb0x, vb0y, vb0z;
    double kTheta, kOmega, kDist;
    double restraintFrc[3];
    double restraintTrq[3];
    double normalize;
    double dVdrx, dVdry, dVdrz;
    double dVdux, dVduy, dVduz;
    double dVdvx, dVdvy, dVdvz;
    double harmPotent;
    double lambdaValue;
    double lambdaK;
    
    char *token;
    char fileName[200];
    char angleName[200];
    char inLine[1000];
    char inValue[200];
    char springName[200];
  };

} // end namespace oopse

#endif
Revision:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years, 6 months ago) by gezelter
File size:	3504 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	Content
1	/*
2	* 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
42	#ifndef _RESTRAINTS_H_
43	#define _RESTRAINTS_H_
44
45	#include <stdlib.h>
46	#include <vector>
47	#include "primitives/Atom.hpp"
48	#include "brains/SimInfo.hpp"
49	#include "io/RestReader.hpp"
50	#include "math/SquareMatrix3.hpp"
51	#include "math/Vector3.hpp"
52
53	namespace oopse {
54
55	class Restraints{
56
57	public:
58	Restraints(SimInfo * info, double lambdaVal, double lambdaExp);
59	~Restraints();
60
61	void Calc_rVal(Vector3d &position, double refPosition[3]);
62	void Calc_body_thetaVal(RotMat3x3d &matrix, double refUnit[3]);
63	void Calc_body_omegaVal(double zAngle);
64	double Calc_Restraint_Forces();
65	double getVharm() { return harmPotent; }
66
67	private:
68	SimInfo * info_;
69	RestReader* restRead_;
70
71	char moleculeName[15];
72
73	int i, j;
74
75	double scaleLam;
76	double delRx, delRy, delRz;
77	double theta, omega;
78	double vProj0[3];
79	double vProjDist;
80	double uTx, uTy, uTz, vTx, vTy, vTz;
81	double ub0x, ub0y, ub0z, vb0x, vb0y, vb0z;
82	double kTheta, kOmega, kDist;
83	double restraintFrc[3];
84	double restraintTrq[3];
85	double normalize;
86	double dVdrx, dVdry, dVdrz;
87	double dVdux, dVduy, dVduz;
88	double dVdvx, dVdvy, dVdvz;
89	double harmPotent;
90	double lambdaValue;
91	double lambdaK;
92
93	char *token;
94	char fileName[200];
95	char angleName[200];
96	char inLine[1000];
97	char inValue[200];
98	char springName[200];
99	};
100
101	} // end namespace oopse
102
103	#endif