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Contents
Index
eFF Programmers' Guide
Julius Su and William A. Goddard III (advisor)
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- Contents
- List of Tables
- License and dependencies
- Recompiling the software
- To modify current features
- To add new features
- To access hidden features
- Function prototypes and data structures
- eff_access
- double GetTotalPE()
- double GetNucleusPE(int i)
- double GetElectronPE(int i)
- void GetNuclearForce(int i, double *fx, double *fy, double *fz)
- void GetElectronForce(int i, double *fx, double *fy, double *fz, double *fr)
- void GetNuclearPosition(int i, double *x, double *y, double *z)
- void SetNuclearPosition(int i, double x, double y, double z)
- void GetElectronPosition(int i, double *x, double *y, double *z, double *r)
- void SetElectronPosition(int i, double x, double y, double z, double r)
- double GetNuclearCharge(int i)
- int GetElectronSpin(int i)
- void SetElectronSpin(int i, int spin)
- int NumNuclei()
- int NumElectrons()
- void AddNuclearForce(int i, double fx, double fy, double fz)
- void AddElectronForce(int i, double fx, double fy, double fz, double fr)
- void AddNucleusPE(int i, double energy)
- void AddElectronPE(int i, double energy)
- void SetNucFX(int i, double val)
- void SetNucFY(int i, double val)
- void SetNucFZ(int i, double val)
- void SetElecFX(int i, double val)
- void SetElecFY(int i, double val)
- void SetElecFZ(int i, double val)
- void SetElecFR(int i, double val)
- eff_bounds
- eff_constants
- eff_create
- eff_driver
- eff_dynamics
- Data structures
- void SetDynamicsLogfile(FILE *fp)
- void AllocateDynamics()
- void SaveDynamics()
- void RevertDynamics()
- void InitializeDynamics()
- void InitializeRandomVelocities(double temp)
- void NullCMMotion()
- void Dynamics(enum ThermostatType s_thermostat, double temperature)
- void UpdateDynamicsPositions()
- void UpdateDynamicsVelocities(enum ThermostatType thermostat, double temperature)
- void ApplyNoseHoover(double temperature)
- void ApplyNoseHooverNuclei(double temperature)
- void GetDynamicsForces()
- void GetDynamicsPositions()
- void SetDynamicsPositions()
- void UpdateDynamicsVirial()
- void SetTimeStep(double dt)
- double GetTemperature()
- void SetNuclearVelocity(int i, double vx, double vy, double vz)
- void SetElectronVelocity(int i, double vx, double vy, double vz, double vr)
- void GetNuclearVelocity(int i, double *vx, double *vy, double *vz)
- void GetElectronVelocity(int i, double *vx, double *vy, double *vz, double *vr)
- void SetNuclearMass(int i, double mx, double my, double mz)
- void SetElectronMass(int i, double mx, double my, double mz, double mr)
- void GetNuclearMass(int i, double *mx, double *my, double *mz)
- void GetElectronMass(int i, double *mx, double *my, double *mz, double *mr)
- double GetTotalKE()
- double GetNucleusKE(int i)
- double GetElectronKE(int i)
- double GetElectronTranslationKE(int i)
- eff_efield
- eff_eigen
- eff_erf
- eff_ewald
- Data structures
- void AllocateEwald()
- void InitializeEwald(double Lx, double Ly, double Lz, double max_alpha, double max_r, double max_k, double nuc_alpha)
- void SetEwaldCharges(double nuc_alpha)
- double TotalCharge()
- double TotalVolume()
- void AddEwaldEnergyForce(double *fx, double *fy, double *fz, double *falpha, double *energy)
- void EwaldVirial(double *ewald_energy, double *ewald_falpha)
- void UpdateEwaldEnergy()
- void InitializeKSpace()
- void InitializeRSpace()
- void KSpaceEnergy(double *fx, double *fy, double *fz, double *falpha, double *energy)
- void RSpaceEnergy(double *fx, double *fy, double *fz, double *falpha, double *energy)
- void SelfEnergy(double *falpha, double *energy)
- void UniformChargeEnergy(double *falpha, double *energy)
- double EwaldRCutoff(double precision, double alpha_cutoff, double min_alpha)
- double EwaldKCutoff(double precision, double alpha_cutoff)
- eff_freeze
- eff_global
- eff_initial
- Data structures
- void AllocateInitialVelocities(int max_nuc_v, int max_elec_v)
- void AllocateInitialMasses(int max_nuc_m, int max_elec_m)
- int GetNumNucV()
- int GetNumElecV()
- int GetNumNucM()
- int GetNumElecM()
- void AddNucV(int i, double vx, double vy, double vz)
- void AddElecV(int i, double vx, double vy, double vz, double vr)
- void GetNucV(int idx, int *i, double *vx, double *vy, double *vz)
- void GetElecV(int idx, int *i, double *vx, double *vy, double *vz, double *vr)
- void AddNucM(int i, double mx, double my, double mz)
- void AddElecM(int i, double mx, double my, double mz, double mr)
- void GetNucM(int idx, int *i, double *mx, double *my, double *mz)
- void GetElecM(int idx, int *i, double *mx, double *my, double *mz, double *mr)
- eff_input
- eff_listint
- eff_listptr
- eff_minimize
- Data structures
- void AllocateMinimize(enum MinimizeType minmethod)
- int MinStorageRequirements(enum MinimizeType minmethod)
- void CalcContractFG(double *x, double *f, double *g)
- enum MinimizeResult Minimize(enum MinimizeType s_minmethod, double eps, double acc, int max_numsteps, int print_every, void (*MinCallback)(int, int, double, double))
- void GetMinimizeForces(double *forces)
- void GetInitialPosition(double *positions)
- void SetMinimizePositions(double *positions)
- eff_output
- eff_params
- eff_pressure
- Data structures
- void ClearVirial()
- void AddForceVirial(double rx, double ry, double rz, double rr, double fx, double fy, double fz, double fr, enum ElectronType electron_type)
- void AddSizeForceVirial(double r, double f, enum ElectronType electron_type)
- void AddRadialForceVirial(double r, double f, enum ElectronType electron_type)
- void AddPotentialEnergyVirial(double energy, enum ElectronType electron_type)
- void AddKineticEnergyVirial(double energy, enum ElectronType electron_type)
- double GetRigidPEPressure(double volume)
- double GetFlexiblePEPressure(double volume)
- double GetRigidKEPressure(double volume)
- double GetFlexibleKEPressure(double volume)
- eff_properties
- eff_restrain
- Data structures
- void InitializeRestraints()
- void ClearRestraints()
- void AddCoordinateRestraint(int idx, double x, double y, double z)
- void AddDistanceRestraint(int idx1, int idx2, double dist)
- void AddAngleRestraint(int idx1, int idx2, int idx3, double angle)
- void AddDihedralRestraint(int idx1, int idx2, int idx3, int idx4, double angle)
- void AddLineRestraint(int *indices, int numindices)
- void AddPlaneRestraint(int *indices, int numindices)
- void AddTetherRestraint(int *indices, int numindices)
- double ApplyRestraints()
- void ApplyTetherVelocityRestraints()
- void AddsNucElecForce(int idx, double fx, double fy, double fz)
- void GetNucElecPosition(int idx, double *x, double *y, double *z)
- void GetNucElecForce(int idx, double *fx, double *fy, double *fz)
- void GetNucElecMass(int idx, double *mx, double *my, double *mz)
- void GetNucElecVelocity(int idx, double *vx, double *vy, double *vz)
- void SetNucElecVelocity(int idx, double vx, double vy, double vz)
- void NucElecString(char *str, int idx)
- double ApplyCoordinateRestraint(int idx, double x0, double y0, double z0, double *dist)
- double ApplyDistanceRestraint(int idx1, int idx2, double dist0, double *dist)
- double ApplyAngleRestraint(int idx1, int idx2, int idx3, double angle0, double *angle)
- double ApplyDihedralRestraint(int idx1, int idx2, int idx3, int idx4, double d0, double *angle)
- double ApplyLineRestraint(int *indices, int numindices, double *dists)
- double ApplyPlaneRestraint(int *indices, int numindices, double *dists)
- double ApplyTetherRestraint(int *indices, int numindices, double *dists)
- double ApplyTetherRestraintVelocity(int *indices, int numindices)
- void OutputRestraints(FILE *out_fp)
- void OutputRestartRestraints(FILE *restart_fp)
- eff_shanno
- int conmin(int n, double *x, double *f, double *g, int *ifun, int *iter, double eps, int mxfun, double *w, int iout, int mdim, double acc, int nmeth, void (*calcfg)(double *, double *, double *), void (*update_func)(int, int, double, double))
- double dmin(double a, double b)
- double dmax(double a, double b)
- eff_timing
- eff_update
- eff_util
- Index
- About this document ...
Julius
2008-04-29