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Index

accessor functions
see eff_access
add_list_int()
void add_list_int(LIST_INT *list, int
add_list_ptr()
eff_listptr
AddAngleRestraint()
void AddAngleRestraint(int idx1, int
AddCoordinateRestraint()
void AddCoordinateRestraint(int idx, double
AddDihedralRestraint()
void AddDihedralRestraint(int idx1, int
AddDistanceRestraint()
void AddDistanceRestraint(int idx1, int
AddElecM()
void AddElecM(int i, double
AddElectron()
int AddElectron(double x, double
AddElectronForce()
void AddElectronForce(int i, double
AddElectronPE()
void AddElectronPE(int i, double
AddElecV()
void AddElecV(int i, double
AddEwaldEnergyForce()
void AddEwaldEnergyForce(double *fx, double
AddForceVirial()
void AddForceVirial(double rx, double
AddFreezeElecR()
void AddFreezeElecR(int i)
AddFreezeElecX()
void AddFreezeElecX(int i)
AddFreezeElecY()
void AddFreezeElecY(int i)
AddFreezeElecZ()
void AddFreezeElecZ(int i)
AddFreezeNucX()
void AddFreezeNucX(int i)
AddFreezeNucY()
void AddFreezeNucY(int i)
AddFreezeNucZ()
void AddFreezeNucZ(int i)
AddKineticEnergyVirial()
void AddKineticEnergyVirial(double energy, enum
AddLineRestraint()
void AddLineRestraint(int *indices, int
AddNuclearForce()
void AddNuclearForce(int i, double
AddNucleus()
int AddNucleus(double x, double
AddNucleusPE()
void AddNucleusPE(int i, double
AddNucM()
void AddNucM(int i, double | void GetNucM(int idx, int
AddNucV()
void AddNucV(int i, double
AddParameter()
void AddParameter(char *name, void
AddParameters()
Add a new parameter
AddPlaneRestraint()
void AddPlaneRestraint(int *indices, int
AddPotentialEnergyVirial()
void AddPotentialEnergyVirial(double energy, enum
AddRadialForceVirial()
void AddRadialForceVirial(double r, double
AddSizeForceVirial()
Kinetic energy | void AddSizeForceVirial(double r, double
AddsNucElecForce()
void AddsNucElecForce(int idx, double
AddTetherRestraint()
void AddTetherRestraint(int *indices, int
AllocateDynamics()
Integration algorithm | void AllocateDynamics()
AllocateEwald()
void AllocateEwald()
AllocateInitialMasses()
void AllocateInitialMasses(int max_nuc_m, int
AllocateInitialVelocities()
void AllocateInitialVelocities(int max_nuc_v, int
AllocateMinimize()
void AllocateMinimize(enum MinimizeType minmethod)
AnnealSpins()
void AnnealSpins(double start_temperature, double
ApplyAngleRestraint()
double ApplyAngleRestraint(int idx1, int
ApplyCoordinateRestraint()
double ApplyCoordinateRestraint(int idx, double
ApplyDihedralRestraint()
double ApplyDihedralRestraint(int idx1, int
ApplyDistanceRestraint()
double ApplyDistanceRestraint(int idx1, int
ApplyExternalField()
void ApplyExternalField(double t)
ApplyFreezes()
void ApplyFreezes()
ApplyLineRestraint()
double ApplyLineRestraint(int *indices, int
ApplyNoseHoover()
void ApplyNoseHoover(double temperature)
ApplyNoseHooverNuclei()
Thermostat | void ApplyNoseHooverNuclei(double temperature)
ApplyPlaneRestraint()
double ApplyPlaneRestraint(int *indices, int
ApplyPositionBounds()
void ApplyPositionBounds()
ApplyRestraints()
Add a new restraint | double ApplyRestraints()
ApplyTetherRestraint()
double ApplyTetherRestraint(int *indices, int
ApplyTetherRestraints()
Add a new restraint
ApplyTetherRestraintVelocity()
double ApplyTetherRestraintVelocity(int *indices, int
ApplyTetherVelocityRestraints()
void ApplyTetherVelocityRestraints()
AssignParticleBins()
void AssignParticleBins()
BFGS
see eff_shanno
boundary
minimum image
eff_update
boundary conditions
see eff_bounds
CalcContractFG()
void CalcContractFG(double *x, double
CalcDipole()
void CalcDipole(double *dipole_x, double
callback function
minimizer
void CalcContractFG(double *x, double
Chebyshev polynomial
eff_erf
clear_list_int
void clear_list_int(LIST_INT *list)
ClearFreezes()
void ClearFreezes()
ClearRestraints()
Add a new restraint | void ClearRestraints()
ClearVirial()
void ClearVirial()
conjugate gradient
see eff_shanno
conmin()
int conmin(int n, double
constraints
see eff_freeze
conversion factors
see eff_constants
CountLines()
int CountLines(FILE *fp, char
CPU time
see CPUTimeElapsed()
CPUTimeElapsed()
double CPUTimeElapsed()
creating particles
see eff_create
data structures
dynamics
Data structures
Ewald
Data structures
freeze
Data structures
initial velocities and masses
Data structures
integer linked list
Data structure
minimize
Data structures
nuclei and electrons
Nucleus data
parameters
Data structures
partition space
Data structures
pressure virial
Data structures
restraints
Data structures
void pointer linked list
see eff_listptr
degrees of freedom
add new
Add more degrees of
issues with too many
Our experience
delete_list_int()
void delete_list_int(LIST_INT *list)
delete_list_ptr()
eff_listptr
dipole moment
see eff_properties
dmax()
double dmax(double a, double
dmin()
double dmin(double a, double
dyn_prev_f
Data structures
dyn_x/v/f
Data structures
dynamic particle creation
Create and destroy particles
dynamics
see eff_dynamics
Dynamics()
void Dynamics(enum ThermostatType s_thermostat,
eff_access
eff_access
eff_bounds
eff_bounds
eff_constants
eff_constants
eff_create
eff_create
eff_driver
eff_driver
eff_dynamics
eff_dynamics
eff_efield
eff_efield
eff_eigen
eff_eigen
eff_erf
eff_erf
eff_ewald
eff_ewald
eff_freeze
eff_freeze
eff_global
eff_global
eff_initial
eff_initial
eff_input
eff_input
eff_listint
eff_listint
eff_listptr
eff_listptr
eff_minimize
eff_minimize
eff_output
eff_output
eff_params
eff_params
eff_pressure
eff_pressure
eff_properties
eff_properties
eff_restrain
eff_restrain
eff_shanno
eff_shanno
eff_timing
eff_timing
eff_update
eff_update
eff_util
eff_util
eigenvalues and eigenvectors
see eff_eigen
elec[]
Nucleus data
ElecElecElec()
Non-Ewald electrostatics
ElecNucElec()
Non-Ewald electrostatics
ElecNucNuc()
Non-Ewald electrostatics
electric field
see eff_efield
electron density
see eff_properties
ElectronDensity()
double ElectronDensity(double x, double
electrostatic energy
seeeff_update
eff_update
electrostatics
Ewald
see eff_ewald
real space
void RSpaceEnergy(double *fx, double
real space cutoff
double EwaldRCutoff(double precision, double
reciprocal space
void KSpaceEnergy(double *fx, double
reciprocal space cutoff
double EwaldKCutoff(double precision, double
self energy
void SelfEnergy(double *falpha, double
uniform charge
void UniformChargeEnergy(double *falpha, double
modify Ewald
Ewald electrostatics
modify non-Ewald
Non-Ewald electrostatics
energy/force calculation
seeeff_update
eff_update
erfoverx()
double erfoverx(double x)
erfoverx1()
double erfoverx1(double x, double
erfoverx2()
double erfoverx2(double x, double
error function
see eff_erf
error()
void error(const char *format,
ewald_fx/fy/fz/falpha
Data structures
ewald_S_cap_real/imag
Data structures
ewald_S_real/imag
Data structures
ewald_x/y/z/alpha/q
Data structures
EwaldKCutoff
double EwaldKCutoff(double precision, double
EwaldRCutoff
double EwaldRCutoff(double precision, double
EwaldVirial()
Ewald electrostatics | void EwaldVirial(double *ewald_energy, double
ExecuteParameter()
void ExecuteParameter(char *name, int
freeze_elec_x/y/z/r
Data structures
freeze_nuc_x/y/z
Data structures
frozen coordinates
see eff_freeze
GetBasename()
void GetBasename(char *str, char
GetDynamicsForces()
void GetDynamicsForces()
GetDynamicsPositions()
void GetDynamicsPositions()
GetElecM()
void GetElecM(int idx, int
GetElectronForce()
void GetElectronForce(int i, double
GetElectronKE()
double GetElectronKE(int i)
GetElectronMass()
void GetElectronMass(int i, double
GetElectronPE()
double GetElectronPE(int i)
GetElectronPosition()
void GetElectronPosition(int i, double
GetElectronSpin()
int GetElectronSpin(int i)
GetElectronTranslationKE()
double GetElectronTranslationKE(int i)
GetElectronVelocity()
void GetElectronVelocity(int i, double
GetElecV()
void GetElecV(int idx, int
GetExtension()
void GetExtension(char *str, char
GetExternalField()
void GetExternalField(double t, double
GetFlexibleKEPressure()
double GetFlexibleKEPressure(double volume)
GetFlexiblePEPressure()
double GetFlexiblePEPressure(double volume)
GetInitialPosition()
void GetInitialPosition(double *positions)
GetMass()
double GetMass(int Z)
GetMinimizeForces()
void GetMinimizeForces(double *forces)
GetNucElecForce()
void GetNucElecForce(int idx, double
GetNucElecMass()
void GetNucElecMass(int idx, double
GetNucElecPosition()
void GetNucElecPosition(int idx, double
GetNucElecVelocity()
void GetNucElecVelocity(int idx, double
GetNuclearCharge()
double GetNuclearCharge(int i)
GetNuclearForce()
void GetNuclearForce(int i, double
GetNuclearMass()
void GetNuclearMass(int i, double
GetNuclearPosition()
void GetNuclearPosition(int i, double
GetNuclearVelocity()
void GetNuclearVelocity(int i, double
GetNucleusKE()
double GetNucleusKE(int i)
GetNucleusPE()
double GetNucleusPE(int i)
GetNucV()
void GetNucV(int idx, int
GetNumElecM()
int GetNumElecM()
GetNumElecV()
int GetNumElecV()
GetNumNucM()
int GetNumNucM()
GetNumNucV()
int GetNumNucV()
GetRigidKEPressure()
double GetRigidKEPressure(double volume)
GetRigidPEPressure()
double GetRigidPEPressure(double volume)
GetTemperature()
double GetTemperature()
GetTotalKE()
double GetTotalKE()
GetTotalPE()
double GetTotalPE()
GetType()
char *GetType(int Z)
GetVolume()
double GetVolume()
GetZ()
int GetZ(char *str)
global parameters
see eff_global
ierfoverx1()
Non-Ewald electrostatics
initial velocities and masses
see eff_initial
Initialize()
void Initialize(int maxnuclei, int
InitializeBounds()
void InitializeBounds()
InitializeDynamics()
void InitializeDynamics()
InitializeEwald()
void InitializeEwald(double Lx, double
InitializeFreezes()
void InitializeFreezes()
InitializeKSpace()
void InitializeKSpace()
InitializeParameters()
void InitializeParameters()
InitializeRandomVelocities()
void InitializeRandomVelocities(double temp)
InitializeRestraints()
Add a new restraint | void InitializeRestraints()
InitializeRSpace()
void InitializeRSpace()
input file parser
see eff_input
integrator
modify
Integration algorithm
IntitializeEnergyUpdater()
void IntitializeEnergyUpdater()
isWrapX()
int isWrapX()
isWrapY()
int isWrapY()
isWrapZ()
int isWrapZ()
jacobi iteration
see eff_eigen
jacobi()
void jacobi(double *matrix, double
K_ANGLE
Data structures
K_COORD
Data structures
K_DIHEDRAL
Data structures
K_DISTANCE
Data structures
K_LINE
Data structures
K_PLANE
Data structures
kinetic energy
double GetTotalKE()
modify
Kinetic energy
seeeff_update
eff_update
KSpaceEnergy()
Ewald electrostatics | void KSpaceEnergy(double *fx, double
lattice_kx/y/z/2
Data structures
lattice_rx/y/z
Data structures
lcase()
void lcase(char *str)
LeftStencil()
int LeftStencil(int numbins, int
license
License
linked list
integer
see eff_listint
void pointers
see eff_listptr
main loop
see eff_driver
Maxwell-Boltzmann distribution
void InitializeRandomVelocities(double temp)
min()
double min(double x, double
min_temp
Data structures
min_x/f/g
Data structures
minimize
see eff_minimize
Minimize()
enum MinimizeResult Minimize(enum MinimizeType
MinimizeCallback()
void MinimizeCallback(int num_iterations, int
MinStorageRequirements()
int MinStorageRequirements(enum MinimizeType minmethod)
new_list_int()
LIST_INT *new_list_int()
new_list_ptr()
eff_listptr
nuc[]
Nucleus data
NucElecIndex()
void NucElecIndex(char *str, int
NucElecString()
void NucElecString(char *str, int
nuclear-electron orbital
see protons
NullCMMotion()
void NullCMMotion()
NumElectrons()
int NumElectrons()
numerical derivatives
Check analytic derivatives | void PrintNumericalForces()
NumNuclei()
int NumNuclei()
orthogonalization
implicit vs explicit
Add more degrees of
OutputEnergy()
Add a new property | void OutputEnergy(FILE *out_fp)
OutputEnergyForces()
void OutputEnergyForces(FILE *out_fp)
OutputFixedHeader()
Add a new parameter | void OutputFixedHeader(FILE *out_fp) | void OutputDynamicsMasses(FILE *out_fp)
OutputParams()
void OutputParams(char *tag, FILE
OutputPositions()
void OutputPositions(FILE *out_fp)
OutputRestartFile()
void OutputRestartFile(char *restart_filname)
OutputRestartRestraints()
Add a new restraint | void OutputRestartRestraints(FILE *restart_fp)
OutputRestraints()
void OutputRestraints(FILE *out_fp)
OutputTimeElapsed()
void OutputTimeElapsed(FILE *out_fp)
OutputVelocities()
void OutputVelocities(FILE *out_fp)
pairwise cutoff
modify
Pairwise cutoff function
ParamAdapativeNumTries
Parsing functions
ParamAdaptiveEnergy
Parsing functions
ParamAdaptiveStepSize
Parsing functions
ParamAndersenCoupling
Parsing functions
ParamCalc
Parsing functions
ParamCutoff
Parsing functions
ParamDt
Parsing functions
ParamEField
Parsing functions
ParamEFieldFreq
Parsing functions
ParamEFieldPacketDuration
Parsing functions
ParamElectronMass
Parsing functions
parameter
add a new
Add a new parameter
eff_params
see eff_params
table with defaults
Parameters
ParamEwald
Parsing functions
ParamMin
Parsing functions
ParamMinFreeze
Parsing functions
ParamNoseHooverCoupling
Parsing functions
ParamNumSteps
Parsing functions
ParamOutput
Parsing functions
ParamPeriodic
Parsing functions
ParamPrintEvery
Parsing functions
ParamRandSeed
Parsing functions
ParamSizeLimit
Parsing functions
ParamSizeLimitStiffness
Parsing functions
ParamTemperature
Parsing functions
ParamThermostat
Parsing functions
ParamXYZBound
Parsing functions
ParseString()
void ParseString(char *buffer, int
parsing functions
Parsing functions
partition
rectangular cells
eff_update
Pauli potential
modify
Pauli potential
seeeff_update
eff_update
PauliElecElec()
Pauli potential
physical constants
see eff_constants
poly01()
double poly01(double x)
poly02()
double poly02(double x)
poly1()
double poly1(double x)
poly2()
double poly2(double x)
pressure
eff_pressure
see eff_pressure
rigid vs flexible
eff_pressure
PrintAnalyticForces()
void PrintAnalyticForces()
PrintNumericalForces()
void PrintNumericalForces()
ProcessElecMasses()
void ProcessElecMasses(char *str)
ProcessElectron()
void ProcessElectron(char *str)
ProcessElecVelocities()
void ProcessElecVelocities(char *str)
ProcessInputFile()
void ProcessInputFile(FILE *fp)
ProcessNucleus()
void ProcessNucleus(char *str)
ProcessNucMasses()
void ProcessNucMasses(char *str)
ProcessNucVelocities()
void ProcessNucVelocities(char *str)
ProcessParam()
void ProcessParam(char *str)
ProcessRestraints()
void ProcessRestraints(char *str)
properties
see eff_properties
property
add a new
Add a new property
protons
floating Gaussian
Make nuclei floating Gaussians
rand_gauss()
double rand_gauss()
rand_int()
int rand_int(int max)
rand_seed()
void rand_seed(unsigned int seed)
rand_uni()
double rand_uni()
ReadValue()
void ReadValue(char *str, double
restraint
add a new
Add a new restraint
angle
void AddAngleRestraint(int idx1, int
coordinate
void AddCoordinateRestraint(int idx, double
dihedral
void AddDihedralRestraint(int idx1, int
distance
void AddDistanceRestraint(int idx1, int
eff_restrain
see eff_restrain
line
void AddLineRestraint(int *indices, int
plane
void AddPlaneRestraint(int *indices, int
tether
eff_restrain | void AddTetherRestraint(int *indices, int
restraint labels
void NucElecIndex(char *str, int
RevertDynamics()
Integration algorithm | void RevertDynamics()
RightStencil()
int RightStencil(int numbins, int
RSpaceEnergy()
Ewald electrostatics | void RSpaceEnergy(double *fx, double
RunDynamics()
void RunDynamics()
RunMinimize()
void RunMinimize()
RunSinglePoint()
void RunSinglePoint()
save_dyn_prev_f
Data structures
save_dyn_x/v/f
Data structures
SaveDynamics()
Integration algorithm | void SaveDynamics()
SelfEnergy()
Ewald electrostatics | void SelfEnergy(double *falpha, double
SetDefaultParameters()
void SetDefaultParameters()
SetDynamicsLogfile()
void SetDynamicsLogfile(FILE *fp)
SetDynamicsPositions()
void SetDynamicsPositions()
SetElecFR()
void SetElecFR(int i, double
SetElecFX()
void SetElecFX(int i, double
SetElecFY()
void SetElecFY(int i, double
SetElecFZ()
void SetElecFZ(int i, double
SetElectronMass()
void SetElectronMass(int i, double
SetElectronPosition()
void SetElectronPosition(int i, double
SetElectronSpin()
void SetElectronSpin(int i, int
SetElectronVelocity()
void SetElectronVelocity(int i, double
SetEwaldCharges()
void SetEwaldCharges(double nuc_alpha)
SetMinimizePositions()
void SetMinimizePositions(double *positions)
SetNucElecVelocity()
void SetNucElecVelocity(int idx, double
SetNucFX()
void SetNucFX(int i, double
SetNucFY()
void SetNucFY(int i, double
SetNucFZ()
void SetNucFZ(int i, double
SetNuclearMass()
void SetNuclearMass(int i, double
SetNuclearPosition()
void SetNuclearPosition(int i, double
SetNuclearVelocity()
void SetNuclearVelocity(int i, double
SetTimeStep()
void SetTimeStep(double dt)
SetupExternalField()
void SetupExternalField(double Ex0, double
Shanno minimizer
Data structures | see eff_shanno
spin annealing
Use spin annealing
StartTimer()
void StartTimer()
StopTimer()
void StopTimer()
stopwatch
see eff_timing
string_match()
int string_match(char *str1, char
StripNewline()
void StripNewline(char *str)
temperature
double GetTemperature()
thermostat
Andersen
eff_dynamics
making a chain
Thermostat
modify
Thermostat
Nose-Hoover
eff_dynamics | void ApplyNoseHoover(double temperature)
TotalCharge()
double TotalCharge()
TotalTimeElapsed()
double TotalTimeElapsed()
TotalVolume()
double TotalVolume()
UniformChargeEnergy()
Ewald electrostatics | void UniformChargeEnergy(double *falpha, double
UpdateDynamicsPositions()
Integration algorithm | void UpdateDynamicsPositions()
UpdateDynamicsVelocities()
Integration algorithm | Thermostat | void UpdateDynamicsVelocities(enum ThermostatType thermostat,
UpdateDynamicsVirial()
void UpdateDynamicsVirial()
UpdateElecAndPauli()
void UpdateElecAndPauli(int bin1, int
UpdateEnergyForces()
void UpdateEnergyForces()
UpdateEwaldEnergy()
void UpdateEwaldEnergy()
UpdateKineticEnergy()
Kinetic energy | void UpdateKineticEnergy()
UpdatePauliPeriodic()
void UpdatePauliPeriodic()
UpdateWidthRestraint()
void UpdateWidthRestraint()
User time
see TotalTimeElapsed()
utility functions
see eff_util
velocity Verlet
see eff_dynamics
velocity Verlet algorithm
void UpdateDynamicsPositions()
writing files
see eff_output



Julius 2008-04-29