Command line

polypbren [OPTIONS]

Options:

-h, --help	Print help message
-v, --verbosity:N	Set the degree of verbosity. Levels are 0,1,2 (default: 0).
-d, --distribution:FILE	Change the distribution file to FILE (default: distrib.in)
-p, --parameters:FILE	Change the distribution file to FILE (default: polypbren.cfg)
--mth, --max-threads:N	Set the maximum of threads to use. 0 means it is auto-detected. (default: 1)
--version	Print version

Input files

The following input files are needed:

• A distribution file (default name is 'distrib.in', use option -d:MyDistribFile to set it), The first line is the number of particle types, denoted n, then it must be n lines of 3 columns: number of particles (integer), radius (nm), and surface charge density (e/nm^2).

  The charge is of course unknown in the case of pH regulation, it can be considered as a first guess (the better it is the faster the convergence will be) .

• A parameter file (default is 'polypbren.cfg', use option -p:MyConfig to set it). It is composed of lines of the form "key = value" , array of values are of the form [val1, val2, ...], comments start with '#'. Examples are given in the examples folder. See also the complete list of parameters below.

The output files are:

• distrib.out : gives the effective surface charges densities (same formatting as the distribution files).
• distrib-bare.out : gives the bare surface charge densities when there is titration.
• peffs.dat : gives, in this order, the volume fraction, the effective inverse screening length (nm^-1), and the osmotic pressure (Pa).
• phi*p*.dat : gives the electrostatic reduced potential profile of particles of type p.

Input parameters

model

Possible values:

• cellmod for the Cell Model
• jellmod for the Renormalized Jellium Model

volume_fraction

Volume fraction to reach iteratively for the Cell Model

extern_potential

Potential at the edge of the cell (or at infinity for the Renormalized Jellium Model)

cell_length

Length of the (initial) cell (- cell radius - particle radius). For the RJM, while the value is infinite in theory, a finite value should be set.

ion_charges

List of charge of the ion species. (Up to 8 species are accepted)

ion_densities

Reservoir of the ion species. The number of items must match the one of IonCharge (Up to 8 species are accepted)

condition

Condition at the surface of the colloid. Set to pH, for titrable surface, and charge otherwise.

ph_input

Sets the input pH (real number)

temperature

Sets the temperature

site_density

Sets the density of titrable sites ont the particle surface.

pka --- Sets the pka of sites.

stern_length

Sets the thickness of the Stern layer (in nm).

space_bin

Sets the space resolution (in nm). Default is 0.05.

max_of_steps

Maximum number of steps to reach volume fraction for the Renormalized Jellium Model or the edge potential for the Cell Model

max_of_iterations

Max number of iterations to reach a given pH or surface charge.

max_of_internal_iterations

Max number of iterations of the internal solver (Poisson-Boltzmann with fixed boundary conditions)

tol_init_value

Sets the tolerance (precision to reach) the titration/charge loop.

tol_inner_loop

Sets the tolerance for the internal loop.

tol_cell_condition

Sets the tolerance for the potential at the edge (Cell Model).

tol_volume_fraction

Sets the tolerance for the potential at the edge (Renormalized Jellium Model).

max_potential_zeff_jellium

For the RJM, sets the maximum potential (in absolute value) at which point a fit is performed to compute the renormalized charges. Default is 0.5.