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Parm section is introduced using the `%parm`

directive.

%parm # potential name comes after the %potential directive %potential potential_name # here follow the parameters for the potential ... # it must end with %end_potential directive %end_potential # another potential can follow %potential potential_name_2 # here follow the parameters for the potential 2 ... %end_potential ... # end the parm section %end

In the parm section, the statements/keywords described in the following text are valid. For every supported potential type (sorted alphabetically), the specific keywords and parameters are given separately and sorted alphabetically as well. In the beginning, some generic parameters are discussed (check the section of a potential of interest to see whether they apply). The examples assume that 2 components were specified in the input file.

In certain cases, pyOZ requires entering only unique combinations of interaction parameters. One of such examples is PMF handling, or hard spheres with hs diameter combinations. Since we are dealing here with pair potentials, it is clear that U(12) = U(21). Therefore, we don’t have to enter all combinations (square of the number of components), but only the unique ones. Their number is N(N+1)/2 and they should be entered in the following order:

`11, 12, 13, ... 1n, 22, 23, ..., 2n, 33, ..., 3n, ..., n(n-1), nn`

## General parameters

pyOZ currently supports the following units of distance, that can be specified together with the respective keyword. Please note that for every interaction potential different distance units can be used. These are automatically converted to pyOZ internal distance units (Å).

- Ångström (Å) – keyword
**A** - meter (m) – keyword
**m** - picometer (pm) – keyword
**pm** - nanometer (nm) – keyword
**nm**

The situation is similar for energy units. For every potential you can specify in which units the energy is given. It is then automatically converted to the internal pyOZ energy units (kT). Energy can be entered using:

- Boltzmann factor units (kT) – keyword
**kT** - electronvolts (eV) – keyword
**eV** - kcal/mol – keyword
**kcal_mol** - kJ/mol – keyword
**kj_mol**

pot_title *potential_title*

For every interaction potential, you can specify additional title, which will be used later in the output (at the moment with osmotic coefficient). If you do not specify this keyword, the potential name as defined in pyOZ will be used.

## Coulomb potential, charge-induced dipole interaction

The Coulomb potential can be specified as follows:

%potential Coulomb pot_title Coulomb potential charge 1.0 -1.0 chg_inddip dip_alpha 1.0 2.0 %end_potential

charge *charges*

List of charges for all components, separated by whitespace characters. Uses elementary charge units.

default: none, **mandatory parameter**

allowed values: real

erf_alpha *erf_alpha_value*

This keyword controls the value to be used as a parameter of the erf-function in the Ng-renormalization scheme. Do not change it unless you know what you are doing.

default: calculated automatically from the Debye screening length

allowed values: any

chg_inddip

Turn on the charge-induced dipole interaction.

default: disabled

dip_alpha *excess polarizabilities*

List of excess polarizabilities for all components, separated by whitespace characters. Uses as units.

default: none, **mandatory parameter**

allowed values: real

## Hard spheres potential

The respective section of the input file for hard spheres potential is shown below:

%potential HS pot_title Hard spheres potential hs_diameter 4.0 6.0 #hs_diam_comb 4.0 5.0 6.0 hs_unit A %end_potential

hs_diameter *hs_diameters*

List of hard sphere diameters σ(ii) for all components, separated by whitespace characters. Diameters are given in units defined by hs_unit keyword. Indicated by `hs radii (Angstroms, calc.)`

in the output file. Conflicts with hs_diam_comb.

default: none, **mandatory parameter**

allowed values: real > 0

hs_diam_comb *hs_diameter_combinations*

List of all unique hard sphere diameters (contact distances) σ(ij), separated by whitespace characters. Ordering is described above. Diameters (distances) are given in units defined by hs_unit keyword. Indicated by `hs radii (Angstroms, direct)`

in the output file. Conflicts with hs_diameter

default: none, **mandatory parameter**

allowed values: real > 0

hs_unit *distance_unit*

Specifies the distance unit for σ.

default: A – Ångström

allowed values: see above

## Lennard-Jones potential

For the Lennard-Jones potential the following keywords are valid:

%potential LJ pot_title Lennard-Jones potential sigma 0.4 0.6 sigma_unit nm sigma_rule arit epsilon 0.1 0.1 epsilon_unit kJ_mol epsilon_rule geom %end_potential

epsilon *epsilon_values*

List of depth of minima on the LJ curve (ϵ) for all components, separated by whitespace characters in units defined by epsilon_unit keyword.

default: none, **mandatory parameter**

allowed values: real

epsilon_rule *combination_rule*

The combination rule to be used for calculation of epsilon values corresponding to interaction of different species.

default: geom – geometric average

allowed values: arit (arithmetic average) | geom (geometric average)

epsilon_unit *energy_unit*

Specifies the energy unit for ϵ.

default: kT

allowed values: see above

sigma *sigma_values*

List of distances σ where the respective potential is zero for all components, separated by whitespace characters. Distances are given in units defined by sigma_unit keyword.

default: none, **mandatory parameter**

allowed values: real > 0

sigma_comb *combination_rule*

Combination rule that will be used for evaluation of σ cross-terms.

default: arit – arithmetic average

allowed values: arit (arithmetic average) | geom (geometric average)

sigma_unit *distance_unit*

Specifies the distance unit for σ.

default: A – Ångström

allowed values: see above

## Potential of Mean Force

The PMF is defined as follows:

%potential PMF pot_title Potential of Mean Force from pmf_md.dat pmf_filename pmf_md.dat # or #pmf_filenames c11.dat c12.dat ... c1n.dat c22.dat ... c2n.dat ... c33.dat ... cnn.dat pmf_unit kT lineskip 5 pmf_before Inf pmf_after 0.0 interp_type cosine %end_potential

interp_type *interpolation_type*

Procedure to be used for interpolation of PMF data.

default: linear – linear interpolation

allowed values: linear | cosine

lineskip *lines_to_skip*

Number of lines to be skipped in the file with PMF data. Useful to skip the comments that can be present in the file.

default: 0

allowed values: integer ≥ 0

pmf_after *distance_unit*

Energy to be used for PMF after the region where it is defined.

default: Inf

allowed values: real or Inf (infinity)

pmf_before *energy_value*

Energy to be used for PMF before the region where it is defined.

default: Inf

allowed values: real or Inf (infinity)

Name of the file with the PMF. The file should contain the interaction parameters corresponding to the combinations of components in the order described above. Extra data on line lead to warning messages.

default: none, **mandatory parameter**, mutually exclusive with pmf_filenames

allowed values: valid filename

pmf_filenames *list_of_file_names*

List of files containing the individual PMF combinations, sorted in the order described above. The files are allowed to have only 2 columns (r and PMF), further data lead to warning messages.

default: none, **mandatory parameter**, mutually exclusive with pmf_filename

allowed values: valid filename

pmf_unit *energy_unit*

Specifies the energy unit for the PMF.

default: kT

allowed values: see above

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