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> |
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 |
< |
#include "Atom.hpp" |
54 |
< |
#include "SimState.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 |
< |
//#include "SimInfo.hpp" |
17 |
< |
//#include "ReadWrite.hpp" |
101 |
> |
} // end namespace oopse |
102 |
|
|
19 |
– |
class Restraints{ |
20 |
– |
|
21 |
– |
public: |
22 |
– |
Restraints(double lambdaVal, double lambdaExp); |
23 |
– |
~Restraints(); |
24 |
– |
|
25 |
– |
void Calc_rVal(double position[3], int currentMol); |
26 |
– |
void Calc_body_thetaVal(double matrix[3][3], int currentMol); |
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 |
– |
double getVharm(); |
32 |
– |
|
33 |
– |
private: |
34 |
– |
char moleculeName[15]; |
35 |
– |
|
36 |
– |
int i, j; |
37 |
– |
|
38 |
– |
double scaleLam; |
39 |
– |
double delRx, delRy, delRz; |
40 |
– |
double theta, omega; |
41 |
– |
double vProj0[3]; |
42 |
– |
double vProjDist; |
43 |
– |
double uTx, uTy, uTz, vTx, vTy, vTz; |
44 |
– |
double ub0x, ub0y, ub0z, vb0x, vb0y, vb0z; |
45 |
– |
double kTheta, kOmega, kDist; |
46 |
– |
double restraintFrc[3]; |
47 |
– |
double restraintTrq[3]; |
48 |
– |
double normalize; |
49 |
– |
double dVdrx, dVdry, dVdrz; |
50 |
– |
double dVdux, dVduy, dVduz; |
51 |
– |
double dVdvx, dVdvy, dVdvz; |
52 |
– |
double harmPotent; |
53 |
– |
double lambdaValue; |
54 |
– |
double lambdaK; |
55 |
– |
|
56 |
– |
vector<double> cofmPosX; |
57 |
– |
vector<double> cofmPosY; |
58 |
– |
vector<double> cofmPosZ; |
59 |
– |
vector<double> ubX0; |
60 |
– |
vector<double> uX0; |
61 |
– |
vector<double> ubY0; |
62 |
– |
vector<double> uY0; |
63 |
– |
vector<double> ubZ0; |
64 |
– |
vector<double> uZ0; |
65 |
– |
vector<double> vbX0; |
66 |
– |
vector<double> vX0; |
67 |
– |
vector<double> vbY0; |
68 |
– |
vector<double> vY0; |
69 |
– |
vector<double> vbZ0; |
70 |
– |
vector<double> vZ0; |
71 |
– |
|
72 |
– |
// SimInfo *info; // all the info we'll ever need |
73 |
– |
// Atom **atoms; /* array of atom pointers */ |
74 |
– |
// DirectionalAtom* dAtom; |
75 |
– |
// SimInfo *againInfo; // all the info we'll ever need |
76 |
– |
|
77 |
– |
char *token; |
78 |
– |
char fileName[200]; |
79 |
– |
char angleName[200]; |
80 |
– |
char inLine[1000]; |
81 |
– |
char inValue[200]; |
82 |
– |
char springName[200]; |
83 |
– |
}; |
84 |
– |
|
103 |
|
#endif |