forked from lijiext/lammps
170 lines
6.5 KiB
Plaintext
170 lines
6.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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group command :h3
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[Syntax:]
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group ID style args :pre
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ID = user-defined name of the group :ulb,l
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style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
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{subtract} or {union} or {intersect} :l
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{delete} = no args
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{region} args = region-ID
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{type} or {id} or {molecule}
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args = list of one or more atom types, atom IDs, or molecule IDs
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any entry in list can be a sequence formatted as A:B or A:B:C where
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A = starting index, B = ending index,
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C = increment between indices, 1 if not specified
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args = logical value
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logical = "<" or "<=" or ">" or ">=" or "==" or "!="
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value = an atom type or atom ID or molecule ID (depending on {style})
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args = logical value1 value2
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logical = "<>"
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value1,value2 = atom types or atom IDs or molecule IDs (depending on {style})
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{variable} args = variable-ID
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{subtract} args = two or more group IDs
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{union} args = one or more group IDs
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{intersect} args = two or more group IDs :pre
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:ule
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[Examples:]
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group edge region regstrip
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group water type 3 4
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group sub id 10 25 50
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group sub id 10 25 50 500:1000
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group sub id 100:10000:10
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group sub id <= 150
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group polyA molecule <> 50 250
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group hienergy variable eng
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group boundary subtract all a2 a3
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group boundary union lower upper
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group boundary intersect upper flow
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group boundary delete :pre
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[Description:]
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Identify a collection of atoms as belonging to a group. The group ID
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can then be used in other commands such as "fix"_fix.html,
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"compute"_compute.html, "dump"_dump.html, or "velocity"_velocity.html
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to act on those atoms together.
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If the group ID already exists, the group command adds the specified
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atoms to the group.
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The {delete} style removes the named group and un-assigns all atoms
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that were assigned to that group. Since there is a restriction (see
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below) that no more than 32 groups can be defined at any time, the
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{delete} style allows you to remove groups that are no longer needed,
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so that more can be specified. You cannot delete a group if it has
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been used to define a current "fix"_fix.html or "compute"_compute.html
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or "dump"_dump.html.
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The {region} style puts all atoms in the region volume into the group.
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Note that this is a static one-time assignment. The atoms remain
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assigned (or not assigned) to the group even in they later move out of
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the region volume.
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The {type}, {id}, and {molecule} styles put all atoms with the
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specified atom types, atom IDs, or molecule IDs into the group. These
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3 styles can use arguments specified in one of two formats.
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The first format is a list of values (types or IDs). For example, the
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2nd command in the examples above puts all atoms of type 3 or 4 into
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the group named {water}. Each entry in the list can be a
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colon-separated sequence A:B or A:B:C, as in two of the examples
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above. A "sequence" generates a sequence of values (types or IDs),
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with an optional increment. The first example with 500:1000 has the
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default increment of 1 and would add all atom IDs from 500 to 1000
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(inclusive) to the group sub, along with 10,25,50 since they also
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appear in the list of values. The second example with 100:10000:10
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uses an increment of 10 and would thus would add atoms IDs
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100,110,120, ... 9990,10000 to the group sub.
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The second format is a {logical} followed by one or two values (type
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or ID). The 7 valid logicals are listed above. All the logicals
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except <> take a single argument. The 3rd example above adds all
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atoms with IDs from 1 to 150 to the group named {sub}. The logical <>
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means "between" and takes 2 arguments. The 4th example above adds all
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atoms belonging to molecules with IDs from 50 to 250 (inclusive) to
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the group named polyA.
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The {variable} style evaluates a variable to determine which atoms to
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add to the group. It must be an "atom-style variable"_variable.html
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previously defined in the input script. If the variable evaluates
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to a non-zero value for a particular atom, then that atom is added
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to the specified group.
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Atom-style variables can specify formulas that include thermodynamic
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quantities, per-atom values such as atom coordinates, or per-atom
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quantities calculated by computes, fixes, or other variables. They
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can also include Boolean logic where 2 numeric values are compared to
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yield a 1 or 0 (effectively a true or false). Thus using the
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{variable} style, is a general way to flag specific atoms to include
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or exclude from a group.
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For example, these lines define a variable "eatom" that calculates the
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potential energy of each atom and includes it in the group if its
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potential energy is above the threshhold value -3.0.
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compute 1 all pe/atom
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compute 2 all reduce sum c_1
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thermo_style custom step temp pe c_2
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run 0 :pre
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variable eatom atom "c_1 > -3.0"
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group hienergy variable eatom :pre
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Note that these lines
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compute 2 all reduce sum c_1
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thermo_style custom step temp pe c_2
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run 0 :pre
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are necessary to insure that the "eatom" variable is current when the
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group command invokes it. Because the eatom variable computes the
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per-atom energy via the pe/atom compute, it will only be current if a
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run has been performed which evaluated pairwise energies, and the
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pe/atom compute was actually invoked during the run. Printing the
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thermodyanmic info for compute 2 insures that this is the case, since
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it sums the pe/atom compute values (in the reduce compute) to output
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them to the screen. See the "Variable Accuracy" section of the
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"variable"_variable.html doc page for more details on insuring that
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variables are current when they are evaluated between runs.
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The {subtract} style takes a list of two or more existing group names
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as arguments. All atoms that belong to the 1st group, but not to any
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of the other groups are added to the specified group.
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The {union} style takes a list of one or more existing group names as
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arguments. All atoms that belong to any of the listed groups are
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added to the specified group.
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The {intersect} style takes a list of two or more existing group names
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as arguments. Atoms that belong to every one of the listed groups are
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added to the specified group.
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A group with the ID {all} is predefined. All atoms belong to this
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group. This group cannot be deleted.
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[Restrictions:]
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There can be no more than 32 groups defined at one time, including
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"all".
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[Related commands:]
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"dump"_dump.html, "fix"_fix.html, "region"_region.html,
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"velocity"_velocity.html
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[Default:]
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All atoms belong to the "all" group.
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