StepParam_t Struct Reference

Parameters for configuring Step class. More...

#include <step.h>

List of all members.

Public Attributes
StepMethod	method
StepOption	options
unsigned long	random_seed
double	timestep
double	initial_temperature
void *	messageObjPtr
int(*	output_message )(void *messageObjPtr, const char *msg)
void *	forceObjPtr
int(*	compute_force )(void *forceObjPtr, double *pe, MD_Dvec *force, const MD_Dvec *pos)
void *	resultsObjPtr
int(*	submit_results )(void *resultsObjPtr, StepSystem *sys)
int32	resultsFreq
int32	init_stepnum
MD_Atom *	atom
int32	natoms
double	bath_temperature
double	relaxation_time
double	nh_temperature
double	nh_timescale
double	drude_com_temperature
double	drude_bond_temperature
double	drude_com_timescale
double	drude_bond_timescale
int32	drude_multisteps
double	cgmin_dis
double	cgmin_tol
int32	cgmin_eval
double	settle_oh_dist
double	settle_hoh_angle

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Detailed Description

Parameters for configuring Step class.

User must provide values where appropriate, depending on selected method. Must provide callbacks. Retains ownership of topology and force field arrays.

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Member Data Documentation

MD_Atom* StepParam_t::atom

Array of atom data for system. (Only the mass is needed.)

double StepParam_t::bath_temperature

Temperature of the bath (in Kelvin). Can be set to 0.

double StepParam_t::cgmin_dis

Maximum displacement for line search; 1 A works OK.

int32 StepParam_t::cgmin_eval

Maximum number of potential evaluations before giving up; 50 seems to work well in practice.

double StepParam_t::cgmin_tol

Tolerance for line search; 0.01 A seems OK for most systems.

int(* StepParam_t::compute_force)(void *forceObjPtr, double *pe, MD_Dvec *force, const MD_Dvec *pos)

Computes force array for given pos array. Returns 0 for success. Must be provided.

double StepParam_t::drude_bond_temperature

Thermostat temperature for Drude bond displacements, the cold degrees of freedom.

double StepParam_t::drude_bond_timescale

Thermostat timescale. Controls coupling of the bond system to its thermostat. B. Roux recommends 7.07 fs for Drude particles with mass 0.8 AMU, and shorter for smaller mass values.

double StepParam_t::drude_com_temperature

Thermostat temperature for atomic COMs (centers of mass), the hot degrees of freedom.

double StepParam_t::drude_com_timescale

Thermostat timescale. Controls coupling of the COM system to its thermostat. B. Roux recommends 100 fs.

int32 StepParam_t::drude_multisteps

Number of multisteps for propagating extended system variables. Must be at least 1. Recommended greater than 1, between 2 and 100.

void* StepParam_t::forceObjPtr

Generic handle passed to compute_force() callback.

int32 StepParam_t::init_stepnum

Gives the initial step number.

double StepParam_t::initial_temperature

Initial temperature (in Kelvin). This is used to initialize velocities unless they are assigned in step_setup().

void* StepParam_t::messageObjPtr

Generic handle passed to output_message() callback.

StepMethod StepParam_t::method

Choose a method for integration or minimization.

int32 StepParam_t::natoms

Number of atoms in array. Used as length for position, velocity, and force arrays.

double StepParam_t::nh_temperature

Nose-Hoover thermostat temperature for canonical ensemble (K). Must be greater than 0.

double StepParam_t::nh_timescale

Nose-Hoover thermostat timescale. Controls coupling of the system to the thermostat. A reasonable choice is 50 fs, the period of a harmonic oscillator.

StepOption StepParam_t::options

Select one or more options by bitwise ORing.

int(* StepParam_t::output_message)(void *messageObjPtr, const char *msg)

Routine to receive messages from Step library.

unsigned long StepParam_t::random_seed

Seed for the random number generator.

double StepParam_t::relaxation_time

Relaxation time to determine coupling to temperature bath. Units in femtoseconds. Need relaxation_time >= timestep. Use of relaxation_time == timestep gives simple velocity rescaling. (Leach recommends 400 fs for timestep==1fs.)

int32 StepParam_t::resultsFreq

Gives number of steps between each submit_results() call.

void* StepParam_t::resultsObjPtr

Generic handle passed to submit_results() callback.

double StepParam_t::settle_hoh_angle

Angle equilibrium length for water H-O-H.

double StepParam_t::settle_oh_dist

Bond equilibrium length for water O-H.

int(* StepParam_t::submit_results)(void *resultsObjPtr, StepSystem *sys)

Collects results at end-of-step intervals. Returns 0 for success. Must be provided.

double StepParam_t::timestep

Time step (in femtoseconds).

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The documentation for this struct was generated from the following file:

• step/step.h

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