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< CENTER > < A HREF = "http://lammps.sandia.gov" > LAMMPS WWW Site< / A > - < A HREF = "Manual.html" > LAMMPS Documentation< / A > - < A HREF = "Section_commands.html#comm" > LAMMPS Commands< / A >
< / CENTER >
< HR >
< H3 > group command
< / H3 >
< P > < B > Syntax:< / B >
< / P >
< PRE > group ID style args
< / PRE >
< UL > < LI > ID = user-defined name of the group
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< LI > style = < I > delete< / I > or < I > region< / I > or < I > type< / I > or < I > id< / I > or < I > molecule< / I > or < I > variable< / I > or < I > subtract< / I > or < I > union< / I > or < I > intersect< / I >
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< PRE > < I > delete< / I > = no args
< I > region< / I > args = region-ID
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< I > type< / I > or < I > id< / I > or < I > molecule< / I >
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args = list of one or more atom types, atom IDs, or molecule IDs
any entry in list can be a sequence formatted as A:B or A:B:C where
A = starting index, B = ending index,
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 < I > style< / I > )
args = logical value1 value2
logical = "< >"
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value1,value2 = atom types or atom IDs or molecule IDs (depending on < I > style< / I > )
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< I > variable< / I > args = variable-ID
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< I > subtract< / I > args = two or more group IDs
< I > union< / I > args = one or more group IDs
< I > intersect< / I > args = two or more group IDs
< / PRE >
< / UL >
< P > < B > Examples:< / B >
< / P >
< PRE > group edge region regstrip
group water type 3 4
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group sub id 10 25 50
group sub id 10 25 50 500:1000
group sub id 100:10000:10
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group sub id < = 150
group polyA molecule < > 50 250
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group hienergy variable eng
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group boundary subtract all a2 a3
group boundary union lower upper
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group boundary intersect upper flow
group boundary delete
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< / PRE >
< P > < B > Description:< / B >
< / P >
< P > 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 < A HREF = "fix.html" > fix< / A > ,
< A HREF = "compute.html" > compute< / A > , < A HREF = "dump.html" > dump< / A > , or < A HREF = "velocity.html" > velocity< / A >
to act on those atoms together.
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< / P >
< P > If the group ID already exists, the group command adds the specified
atoms to the group.
< / P >
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< P > The < I > delete< / I > style removes the named group and un-assigns all atoms
that were assigned to that group. Since there is a restriction (see
below) that no more than 32 groups can be defined at any time, the
< I > delete< / I > style allows you to remove groups that are no longer needed,
so that more can be specified. You cannot delete a group if it has
been used to define a current < A HREF = "fix.html" > fix< / A > or < A HREF = "compute.html" > compute< / A >
or < A HREF = "dump.html" > dump< / A > .
< / P >
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< P > The < I > region< / I > style puts all atoms in the region volume into the group.
Note that this is a static one-time assignment. The atoms remain
assigned (or not assigned) to the group even in they later move out of
the region volume.
< / P >
< P > The < I > type< / I > , < I > id< / I > , and < I > molecule< / I > styles put all atoms with the
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.
< / P >
< P > 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 < I > water< / I > . Each entry in the list can be a
colon-separated sequence A:B or A:B:C, as in two of the examples
above. A "sequence" generates a sequence of values (types or IDs),
with an optional increment. The first example with 500:1000 has the
default increment of 1 and would add all atom IDs from 500 to 1000
(inclusive) to the group sub, along with 10,25,50 since they also
appear in the list of values. The second example with 100:10000:10
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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< / P >
< P > The second format is a < I > logical< / I > followed by one or two values (type
or ID). The 7 valid logicals are listed above. All the logicals
except < > take a single argument. The 3rd example above adds all
atoms with IDs from 1 to 150 to the group named < I > sub< / I > . The logical < >
means "between" and takes 2 arguments. The 4th example above adds all
atoms belonging to molecules with IDs from 50 to 250 (inclusive) to
the group named polyA.
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< / P >
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< P > The < I > variable< / I > style evaluates a variable to determine which atoms to
add to the group. It must be an < A HREF = "variable.html" > atom-style variable< / A >
previously defined in the input script. If the variable evaluates
to a non-zero value for a particular atom, then that atom is added
to the specified group.
< / P >
< P > Atom-style variables can specify formulas that include thermodynamic
quantities, per-atom values such as atom coordinates, or per-atom
quantities calculated by computes, fixes, or other variables. They
can also include Boolean logic where 2 numeric values are compared to
yield a 1 or 0 (effectively a true or false). Thus using the
< I > variable< / I > style, is a general way to flag specific atoms to include
or exclude from a group.
< / P >
< P > For example, these lines define a variable "eatom" that calculates the
potential energy of each atom and includes it in the group if its
potential energy is above the threshhold value -3.0.
< / P >
< PRE > compute 1 all pe/atom
compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0
< / PRE >
< PRE > variable eatom atom "c_1 > -3.0"
group hienergy variable eatom
< / PRE >
< P > Note that these lines
< / P >
< PRE > compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0
< / PRE >
< P > are necessary to insure that the "eatom" variable is current when the
group command invokes it. Because the eatom variable computes the
per-atom energy via the pe/atom compute, it will only be current if a
run has been performed which evaluated pairwise energies, and the
pe/atom compute was actually invoked during the run. Printing the
thermodyanmic info for compute 2 insures that this is the case, since
it sums the pe/atom compute values (in the reduce compute) to output
them to the screen. See the "Variable Accuracy" section of the
< A HREF = "variable.html" > variable< / A > doc page for more details on insuring that
variables are current when they are evaluated between runs.
< / P >
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< P > The < I > subtract< / I > style takes a list of two or more existing group names
as arguments. All atoms that belong to the 1st group, but not to any
of the other groups are added to the specified group.
< / P >
< P > The < I > union< / I > style takes a list of one or more existing group names as
arguments. All atoms that belong to any of the listed groups are
added to the specified group.
< / P >
< P > The < I > intersect< / I > style takes a list of two or more existing group names
as arguments. Atoms that belong to every one of the listed groups are
added to the specified group.
< / P >
< P > A group with the ID < I > all< / I > is predefined. All atoms belong to this
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group. This group cannot be deleted.
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< / P >
< P > < B > Restrictions:< / B >
< / P >
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< P > There can be no more than 32 groups defined at one time, including
"all".
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< / P >
< P > < B > Related commands:< / B >
< / P >
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< P > < A HREF = "dump.html" > dump< / A > , < A HREF = "fix.html" > fix< / A > , < A HREF = "region.html" > region< / A > ,
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< A HREF = "velocity.html" > velocity< / A >
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< / P >
< P > < B > Default:< / B >
< / P >
< P > All atoms belong to the "all" group.
< / P >
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