group group_name style_cg style_at group_shape x lower_b upper_b i j k y lower_b upper_b i j k z lower_b upper_b i j k boolean_in group_axis group_centroid_x group_centroid_y group_centroid_z group_radius_large group_radius_small
group_name= a string (length <= 30)
style_cg= element or node or null
style_at= atom or null
group_shape= block or cylinder or cone or tube or sphere
upper_b= real number or inf
k= real number
boolean_in= t or f
t is true f is false
group_axis= 1 or 2 or 3
group_centroid_z= real number
group_radius_small= positive real number
group top_box null atom block x inf inf 1. 0. 0. y inf inf 0. 1. 0. z 14.4 inf 0. 0. 1. t 3 20. 5. 0. 10. 10. group cylin node null cylinder x inf inf 1. 0. 0. y inf inf 0. 1. 0. z 14.4 inf 0. 0. 1. f 3 20. 5. 0. 10. 10. group red_cone element atom cone x inf inf 1. 0. 0. y inf inf 0. 1. 0. z 14.4 inf 0. 0. 1. t 3 20. 5. 0. 10. 5. group big_sphere element null sphere x inf inf 1. 0. 0. y inf inf 0. 1. 0. z 14.4 inf 0. 0. 1. t 3 20. 5. 0. 10. 10.
This command sets new groups, the number of which is provided in the group_num command. The elements/nodes/atoms in a group, either a new group or a restar group, can be moved at each simulation step, deformed with the simulation cell (when
boolean_def in both fix and deform commands = t), or not moved/deformed. The syntax is similar to the first of that of the modify command.
Different new groups cannot have the same
group_name. Also, since the restart groups are automatically named
* is a positive integer starting from
new_group_number + 1, the
group_name in this command cannot have any of those names.
style_cg decides whether the group contains elements (element), nodes (node), or nothing (null) in the coarse-grained domain; the differences between element and node are discussed here.
style_at decides whether the group contains atoms (atom) or nothing (null) in the atomistic domain.
There are currently five
group_shape: block, cylinder, cone, tube, and sphere.
upper_b are the lower and upper boundaries of the
group_shape, respectively, in units of the component of the lattice periodicity length vector along the corresponding direction. When
upper_b = inf, the corresponding lower or upper simulation cell boundaries are taken as the
group_shape boundaries, respectively. Note that when
group_shape = cylinder or cone or tube,
upper_b are the lower and upper plane boundaries normal to the central axis
group_axis direction, respectively.
k decide the
group_shape ( sphere) boundary plane orientations with respect to the simulation cell, similar to those in the box_dir command.
Note that these five options (
k) are irrelevant when
group_shape = sphere, and when
group_shape = cylinder or cone or tube if the corresponding direction is not
group_axis is irrelevant when
group_shape = block or sphere. However, they need to be provided regardless.
boolean_in = t, elements/nodes/atoms inside the
group_shape belong to the group; otherwise, those outside do.
group_centroid_z, in units of the component of the lattice periodicity length vector and with respect to the lower boundaries of the simulation cell along the corresponding direction, are the coordinates of the center of the base plane of a cylinder or cone or tube, or the center of a sphere. When
group_shape = cylinder or cone or tube, the
group_centroid_* that corresponds to the
group_axis direction becomes irrelevant. For example, when
group_axis = 2,
group_centroid_y can take any real number without affecting the results.
group_radius_large is the base radius of a cylinder, the large base radius of a cone, the outer base radius of a tube, or the radius of a sphere.
group_radius_small, the small base radius of a cone or the inner base radius of a tube, is irrelevant for other
group_radius_small are in units of the maximum lattice periodicity length .
Note that these six options (
group_radius_*) are not relevant when
group_shape = block. Yet, they need to be provided regardless.
There cannot be fewer
group commands than
new_group_number. When there are too many
group commands, those appearing later will be ignored. The
group_name in the cal and fix commands must match that in the current command.
This command becomes irrelevant when
new_group_number = 0.