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Comparing trunk/OOPSE-2.0/src/restraints/Restraints.hpp (file contents):
Revision 1772 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 2101 by chrisfen, Thu Mar 10 15:10:24 2005 UTC

# Line 1 | Line 1
1 < /* This is a fun little patch to do molecular restraints for
2 <   thermodynamic integration of solids.  Use only
3 <   if you really know what you are doing.
4 < */
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>
10 – #include <iostream>
46   #include <vector>
12 –
47   #include "primitives/Atom.hpp"
48 < #include "brains/SimState.hpp"
48 > #include "brains/SimInfo.hpp"
49 > #include "io/RestReader.hpp"
50 > #include "math/SquareMatrix3.hpp"
51 > #include "math/Vector3.hpp"
52  
53 < //#include "brains/SimInfo.hpp"
54 < //#include "io/ReadWrite.hpp"
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 < class Restraints{
101 > } // end namespace oopse
102  
21 – public:
22 –  Restraints(double lambdaVal, double lambdaExp);
23 –  ~Restraints();
24 –
25 –  void Calc_rVal(double position[3], double refPosition[3]);
26 –  void Calc_body_thetaVal(double matrix[3][3], double refUnit[3]);
27 –  void Calc_body_omegaVal(double matrix[3][3], double zAngle);
28 –  double Calc_Restraint_Forces(vector<StuntDouble*> vecParticles);
29 –  //  void Store_Init_Info(vector<StuntDouble*> vecParticles);
30 –  void Write_zAngle_File(vector<StuntDouble*> vecParticles,
31 –                         int currTime,
32 –                         int nIntObj);
33 –  double getVharm();
34 –
35 – private:
36 –  char moleculeName[15];
37 –
38 –  int i, j;
39 –
40 –  double scaleLam;
41 –  double delRx, delRy, delRz;
42 –  double theta, omega;
43 –  double vProj0[3];
44 –  double vProjDist;
45 –  double uTx, uTy, uTz, vTx, vTy, vTz;
46 –  double ub0x, ub0y, ub0z, vb0x, vb0y, vb0z;
47 –  double kTheta, kOmega, kDist;
48 –  double restraintFrc[3];
49 –  double restraintTrq[3];
50 –  double normalize;
51 –  double dVdrx, dVdry, dVdrz;
52 –  double dVdux, dVduy, dVduz;
53 –  double dVdvx, dVdvy, dVdvz;
54 –  double harmPotent;
55 –  double lambdaValue;
56 –  double lambdaK;
57 –
58 –  char *token;
59 –  char fileName[200];
60 –  char angleName[200];
61 –  char inLine[1000];
62 –  char inValue[200];
63 –  char springName[200];
64 – };
65 –
103   #endif

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