Configuration

class Configuration

A Configuration contains both Particle s 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 and 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: dictionary of names and files for different particle types. The dictionary syntax is name1:file_name1,name2:file_name2,etc. If only file_name are provided without names, the names will default to 0, 1, etc. Particle names must be unique. See FileParticle for description of the file required to define particles.

  • add_num_[type name]_particles: add this many particles of given type name. Particles are added with the coordinates in the file, so adding multiple will overlap.

  • 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: comma-separated list of group names. All following arguments of the group are then expected to have the name prepended with an underscore (e.g., “group=oxygen oxygen_site_type=O”).

  • model_param_file: input ModelParam with this file with either a three- or four-column space-separated format on each line as follows: “[parameter] [site type name] [value]” “[parameter] [site type name 1] [site type name 2] [value]” This file can be used to override the otherwise default Lorentz-Berthelot mixing rules. Mixing is always symmetric (e.g., params[i][j] == param[j][i]) Comment lines beginning with the ‘#’ character are ignored.

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

  • [parameter][site type name]: optionally set the [parameter] value of the given site type name. These are applied after (overriding) the above argument for all types.

  • [parameter][site type name 1]_[site type name 2]: optionally set the [parameter] value of the 1-2 mixed type. These are applied after (overriding) the above argument for single types.

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

  • 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.

  • name: set the name of the Configuration (default: 0).