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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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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#ifndef _RESTRAINTS_H_ |
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#define _RESTRAINTS_H_ |
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#include <stdlib.h> |
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#include <iostream> |
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#include <vector> |
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#include "primitives/Atom.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "io/RestReader.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/Vector3.hpp" |
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|
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#include "Atom.hpp" |
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#include "SimState.hpp" |
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namespace oopse { |
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|
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class Restraints{ |
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|
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public: |
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Restraints(SimInfo * info, RealType lambdaVal, RealType lambdaExp); |
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~Restraints(); |
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|
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void Calc_rVal(Vector3d &position, RealType refPosition[3]); |
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void Calc_body_thetaVal(RotMat3x3d &matrix, RealType refUnit[3]); |
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void Calc_body_omegaVal(RealType zAngle); |
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RealType Calc_Restraint_Forces(); |
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RealType getVharm() { return harmPotent; } |
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|
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private: |
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SimInfo * info_; |
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RestReader* restRead_; |
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|
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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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RealType scaleLam; |
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RealType delRx, delRy, delRz; |
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RealType theta, omega; |
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RealType vProj0[3]; |
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RealType vProjDist; |
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RealType uTx, uTy, uTz, vTx, vTy, vTz; |
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RealType ub0x, ub0y, ub0z, vb0x, vb0y, vb0z; |
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RealType kTheta, kOmega, kDist; |
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RealType restraintFrc[3]; |
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RealType restraintTrq[3]; |
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RealType normalize; |
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RealType dVdrx, dVdry, dVdrz; |
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RealType dVdux, dVduy, dVduz; |
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RealType dVdvx, dVdvy, dVdvz; |
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RealType harmPotent; |
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RealType lambdaValue; |
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RealType lambdaK; |
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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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//#include "SimInfo.hpp" |
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//#include "ReadWrite.hpp" |
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} // end namespace oopse |
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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 |
