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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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