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#ifndef _INTEGRATOR_H_ |
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#define _INTEGRATOR_H_ |
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#include <string> |
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#include <vector> |
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SRI.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "ZConsWriter.hpp" |
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using namespace std; |
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const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
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const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm |
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virtual void constrainA( void ); |
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virtual void constrainB( void ); |
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virtual int readyCheck( void ) { return 1; } |
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(); |
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void checkConstraints( void ); |
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void rotate( int axes1, int axes2, double angle, double j[3], |
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double A[3][3] ); |
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ForceFields* myFF; |
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SimInfo *info; // all the info we'll ever need |
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short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
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short int have_target_pressure; |
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}; |
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template<typename T> class ZConstraint : public T { |
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public: |
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ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
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~ZConstraint(); |
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void setZConsTime(double time) {this->zconsTime = time;} |
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void getZConsTime() {return zconsTime;} |
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void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
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void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
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void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
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string getZConsOutput() {return zconsOutput;} |
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virtual void integrate(); |
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#ifdef IS_MPI |
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virtual void update(); //which is called to indicate the molecules' migration |
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#endif |
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protected: |
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enum ZConsState {zcsMoving, zcsFixed}; |
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(void); |
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void zeroOutVel(); |
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void doZconstraintForce(); |
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void doHarmonic(); |
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bool checkZConsState(); |
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bool haveFixedZMols(); |
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bool haveMovingZMols(); |
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double calcZSys(); |
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int isZConstraintMol(Molecule* mol); |
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double zconsTime; |
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double zconsTol; |
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double zForceConst; |
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vector<Molecule*> zconsMols; |
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vector<double> massOfZConsMols; |
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vector<double> kz; |
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vector<ZConsState> states; |
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vector<double> zPos; |
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vector<Molecule*> unconsMols; |
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vector<double> massOfUnconsMols; |
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double totalMassOfUncons; |
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vector<ZConsParaItem>* parameters; |
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vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
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int* indexOfZConsMols; //index of local Z-Constraint Molecules |
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double* fz; |
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int totNumOfUnconsAtoms; |
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int whichDirection; //constraint direction |
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private: |
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string zconsOutput; |
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ZConsWriter* fzOut; |
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double calcMovingMolsCOMVel(); |
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double calcSysCOMVel(); |
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double calcTotalForce(); |
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}; |
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#endif |
