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/* This is a fun little patch to do molecular restraints for |
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thermodynamic integration of solids. Use only |
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if you really know what you are doing. |
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*/ |
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|
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#ifndef _RESTRAINTS_H_ |
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#define _RESTRAINTS_H_ |
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|
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#include <stdlib.h> |
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#include <iostream> |
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#include <vector> |
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|
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#include "primitives/Atom.hpp" |
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#include "brains/SimState.hpp" |
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|
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//#include "brains/SimInfo.hpp" |
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//#include "io/ReadWrite.hpp" |
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|
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class Restraints{ |
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|
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public: |
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Restraints(double lambdaVal, double lambdaExp); |
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~Restraints(); |
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|
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void Calc_rVal(double position[3], int currentMol); |
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void Calc_body_thetaVal(double matrix[3][3], int currentMol); |
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void Calc_body_omegaVal(double matrix[3][3], double zAngle); |
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double Calc_Restraint_Forces(vector<StuntDouble*> vecParticles); |
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void Store_Init_Info(vector<StuntDouble*> vecParticles); |
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void Write_zAngle_File(vector<StuntDouble*> vecParticles); |
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double getVharm(); |
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|
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private: |
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char moleculeName[15]; |
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|
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int i, j; |
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|
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double scaleLam; |
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double delRx, delRy, delRz; |
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double theta, omega; |
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double vProj0[3]; |
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double vProjDist; |
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double uTx, uTy, uTz, vTx, vTy, vTz; |
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double ub0x, ub0y, ub0z, vb0x, vb0y, vb0z; |
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double kTheta, kOmega, kDist; |
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double restraintFrc[3]; |
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double restraintTrq[3]; |
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double normalize; |
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double dVdrx, dVdry, dVdrz; |
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double dVdux, dVduy, dVduz; |
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double dVdvx, dVdvy, dVdvz; |
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double harmPotent; |
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double lambdaValue; |
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double lambdaK; |
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|
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vector<double> cofmPosX; |
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vector<double> cofmPosY; |
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vector<double> cofmPosZ; |
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vector<double> ubX0; |
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vector<double> uX0; |
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vector<double> ubY0; |
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vector<double> uY0; |
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vector<double> ubZ0; |
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vector<double> uZ0; |
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vector<double> vbX0; |
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vector<double> vX0; |
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vector<double> vbY0; |
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vector<double> vY0; |
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vector<double> vbZ0; |
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vector<double> vZ0; |
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|
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// SimInfo *info; // all the info we'll ever need |
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// Atom **atoms; /* array of atom pointers */ |
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// DirectionalAtom* dAtom; |
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// SimInfo *againInfo; // all the info we'll ever need |
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|
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char *token; |
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char fileName[200]; |
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char angleName[200]; |
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char inLine[1000]; |
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char inValue[200]; |
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char springName[200]; |
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}; |
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|
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#endif |
