Configuration

class Configuration

A Configuration contains both the particles and the spatial Domain/boundaries.

For the particles, this includes both the pool of particles which may exist (referred to as particle types) in addition to the particles which physically exist (referred to as particles). The same is true for site types and sites.

Groups of different particle/site types and other metrics may be defined. These groups then define a selection which can be used to distinguish subsets of the configuration (e.g., types of particles). This selection may be further reduced to single particles. These selections are then used to modify a subset of the configuration (e.g., removal and displacement) of a selection of particles/sites.

The spatial domain contains periodic boundaries and cells.

Arguments

The following arguments are parsed in the order listed, regardless of the order input by the user.

  • Domain arguments may be parsed here.

  • physical_constants: optional class_name of PhysicalConstants. These are typically only used in charged interactions to compute the conversion factor between squared charge over distance and energy.

  • particle_type[i]: add the i-th type of particle. The “[i]” is to be substituted for an integer 0, 1, 2, … If only one particle type, the “[i]” is optional.

  • add_particles_of_type[i]: add this many of i-th type particles. The “[i]” is to be substituted for an integer 0, 1, 2, …

  • xyz_file: optionally load FileXYZ if not empty (default: empty). Note that Domain tilt factors are not read by FileXYZ.

  • xyz_euler_file: optionally load FileXYZEuler if not empty (default: empty).

  • group[i]: set the name of the “i”-th group. The “[i]” is to be substituted for an integer 0, 1, 2, … All following arguments of the group are then expected to have the name prepended (e.g., “group0 water water_particle_type 0”).

  • wrap: wrap particle centers within domain (default: true).

  • [parameter]: optionally set the [parameter] of all types to this value. The “[parameter]” is to be substituted for epsilon, sigma, cutoff, etc.

  • [parameter][i]: optionally set the [parameter] of the i-th site type. The “[i]” is to be substituted for an integer 0, 1, 2, … These are applied after (overriding) the above argument for all types.

  • [parameter][i]_[j]: optionally set the [parameter] of the i-j mixed type. The “[i]/[j]” is to be substituted for an integer 0, 1, 2, … These are applied after (overriding) the above argument for single types.

  • [parameter]_mixing_file: override default mixing parameters with this file in the three-column space-separated format of “i j [param]_ij”.

  • set_cutoff_min_to_sigma: if true and cutoff < sigma, cutoff = sigma (default: false). This is typically used for HardSphere models that didn’t specify cutoff.