These applications are used to either generate new or analyze existing molecular structures.
Locates, then sizes cavities according to provided configuration and parameters. pddx is a thread-parallel version of ddx and requires pthreads to run.
-box [ 6.0 6.0 6.0 ] box dimensions
-seed [ 1 ] PRNG seed
-randomize re-seed PRNG
-characteristic_length [ 1.0 ] approximate length scale, e.g. typical atomic radius
-characteristic_energy [ 1.0 ] approximate dimensionless energy scale
-precision_parameter [ 0.001 ] delta value for precision of locating stationary points
-n_steps [ 1000 ] maximum number of steps to attempt before accepting convergence
(roughly reciprocal of precision parameter)
-show_steps list # of steps taken as final column
-verlet_cutoff [ 100.0 ] Square of radius used in determining inclusion in Verlet list
-n [ 1 ] Number of samples to run
-volume_sampling Only use points whose trajectory originated within radius of final ghost particle
-include_center_energy
-min_diameter [ 0.0 ] Only include cavities whose diameter is at least this much.
Lennard-Jones fluid.
[-v] verbose
[-ng] no X11 graphics
[-no_side] don't show side
-T [1] temperature
-fixed_perturbation_length []
-particle_scale []
-N number of particles
-relaxation_allowance
-box box dimensions (triplet)
-fg_color []
-bg_color []
-min_color
-rng_seed [] initialize random number generator with given seed
-randomize initialize random number generator with random seed
-end_mcs [] how many Monte Carlo steps to run
-energy_report_frequency []
-configuration_threshold []
-configuration_frequency []
-input_file_name load configuration from a file
-target_acceptance_ratio [] [0..1) fraction of MC moves to accept
-psi_shift truncated and shifted potential, shift value
-cutoff_sq square of Verlet cutoff radius
Two-point correlation code.
IN: list of x,y,z positions, box dims specified at CL.
OUT: Tabulated radial distribution function.
Takes as input a clustered set of cavities and shifts it around until it's no longer hanging out of the simulation box. Does not perform validation check (all cavities are one cluster) only makes sure that no cavity pair straddles a boundary.
IN: .cav
OUT: .cav