| 1 |
gezelter |
1447 |
/* 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 |
|
|
*/ |
| 5 |
|
|
|
| 6 |
|
|
#ifndef _RESTRAINTS_H_ |
| 7 |
|
|
#define _RESTRAINTS_H_ |
| 8 |
|
|
|
| 9 |
|
|
#include <stdlib.h> |
| 10 |
|
|
#include <iostream> |
| 11 |
|
|
#include <vector> |
| 12 |
|
|
|
| 13 |
|
|
#include "Atom.hpp" |
| 14 |
|
|
#include "SimState.hpp" |
| 15 |
|
|
|
| 16 |
|
|
//#include "SimInfo.hpp" |
| 17 |
|
|
//#include "ReadWrite.hpp" |
| 18 |
|
|
|
| 19 |
|
|
class Restraints{ |
| 20 |
|
|
|
| 21 |
|
|
public: |
| 22 |
|
|
Restraints(int nMol, 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, nMol; |
| 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 |
|
|
|
| 85 |
|
|
#endif |
