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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

Distance units

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

Energy units

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 \AA^3 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)

pmf_filename filename

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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