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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8728 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-08-28 15:27:10 +00:00
parent ce74a6e8a3
commit 7c21f7a158
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47
doc/group.html
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@ -17,7 +17,7 @@
</PRE>
<UL><LI>ID = user-defined name of the group
<LI>style = <I>delete</I> or <I>region</I> or <I>type</I> or <I>id</I> or <I>molecule</I> or <I>subtract</I> or <I>union</I> or <I>intersect</I>
<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>
<PRE> <I>delete</I> = no args
<I>region</I> args = region-ID
@ -30,6 +30,7 @@
logical = "<>"
value1,value2 = atom types or atom IDs or molecule IDs
(depending on <I>style</I>)
<I>variable</I> args = variable-ID
<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
@ -42,6 +43,7 @@
group water type 3 4
group sub id <= 150
group polyA molecule <> 50 250
group hienergy variable eng
group boundary subtract all a2 a3
group boundary union lower upper
group boundary intersect upper flow
@ -83,6 +85,49 @@ example above adds all atoms with IDs from 1 to 150 to the group named
example above adds all atoms belonging to molecules with IDs from 50
to 250 (inclusive) to the group named polyA.
</P>
<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>
<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.

49
doc/group.txt
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@ -13,8 +13,8 @@ group command :h3
group ID style args :pre
ID = user-defined name of the group :ulb,l
style = {delete} or {region} or {type} or {id} or {molecule} or {subtract} or \
{union} or {intersect} :l
style = {delete} or {region} or {type} or {id} or {molecule} or {variable} or \
{subtract} or {union} or {intersect} :l
{delete} = no args
{region} args = region-ID
{type} or {id} or {molecule}
@ -26,6 +26,7 @@ style = {delete} or {region} or {type} or {id} or {molecule} or {subtract} or \
logical = "<>"
value1,value2 = atom types or atom IDs or molecule IDs
(depending on {style})
{variable} args = variable-ID
{subtract} args = two or more group IDs
{union} args = one or more group IDs
{intersect} args = two or more group IDs :pre
@ -37,6 +38,7 @@ group edge region regstrip
group water type 3 4
group sub id <= 150
group polyA molecule <> 50 250
group hienergy variable eng
group boundary subtract all a2 a3
group boundary union lower upper
group boundary intersect upper flow
@ -78,6 +80,49 @@ example above adds all atoms with IDs from 1 to 150 to the group named
example above adds all atoms belonging to molecules with IDs from 50
to 250 (inclusive) to the group named polyA.
The {variable} style evaluates a variable to determine which atoms to
add to the group. It must be an "atom-style variable"_variable.html
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.
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
{variable} style, is a general way to flag specific atoms to include
or exclude from a group.
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.
compute 1 all pe/atom
compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0 :pre
variable eatom atom "c_1 > -3.0"
group hienergy variable eatom :pre
Note that these lines
compute 2 all reduce sum c_1
thermo_style custom step temp pe c_2
run 0 :pre
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
"variable"_variable.html doc page for more details on insuring that
variables are current when they are evaluated between runs.
The {subtract} 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.

21
doc/variable.html
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@ -762,13 +762,14 @@ references to a compute or fix, and these values were calculated on
the last timestep of a preceeding run, then they will be accessed and
used by the variable and the result will be accurate.
</P>
<P>(2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable requires a quantity from a
<A HREF = "compute.html">compute</A> that is not current, LAMMPS will generate an
error. This means, for example, that such a variable cannot be
evaluated before the first run has occurred. Likewise, in between
runs, such a variable cannot be accessed unless it was evaluated on
the last timestep of the preceding run, e.g. by thermodynamic output.
<P>(2) LAMMPS may not be able to evaluate the variable and will generate
an error message stating so. For example, if the variable requires a
quantity from a <A HREF = "compute.html">compute</A> that is not current, LAMMPS
will generate an error. This means, for example, that such a variable
cannot be evaluated before the first run has occurred. Likewise, in
between runs, such a variable cannot be accessed unless it was
evaluated on the last timestep of the preceding run, e.g. by
thermodynamic output.
</P>
<P>One way to get around this problem is to perform a 0-timestep run
before using the variable. For example, these commands
@ -811,9 +812,9 @@ until a run is performed. Thus if a variable attempts to print this
value before the first run, zeroes will be output. Again, performing
a 0-timestep run before printing the variable has the desired effect.
</P>
<P>(3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence
of commands:
<P>(3) The variable may be evaluated incorrectly and LAMMPS may have no
way to detect this has occurred. Consider the following sequence of
commands:
</P>
<PRE>pair_coeff 1 1 1.0 1.0
run 1000

21
doc/variable.txt
View File

@ -756,13 +756,14 @@ references to a compute or fix, and these values were calculated on
the last timestep of a preceeding run, then they will be accessed and
used by the variable and the result will be accurate.
(2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable requires a quantity from a
"compute"_compute.html that is not current, LAMMPS will generate an
error. This means, for example, that such a variable cannot be
evaluated before the first run has occurred. Likewise, in between
runs, such a variable cannot be accessed unless it was evaluated on
the last timestep of the preceding run, e.g. by thermodynamic output.
(2) LAMMPS may not be able to evaluate the variable and will generate
an error message stating so. For example, if the variable requires a
quantity from a "compute"_compute.html that is not current, LAMMPS
will generate an error. This means, for example, that such a variable
cannot be evaluated before the first run has occurred. Likewise, in
between runs, such a variable cannot be accessed unless it was
evaluated on the last timestep of the preceding run, e.g. by
thermodynamic output.
One way to get around this problem is to perform a 0-timestep run
before using the variable. For example, these commands
@ -805,9 +806,9 @@ until a run is performed. Thus if a variable attempts to print this
value before the first run, zeroes will be output. Again, performing
a 0-timestep run before printing the variable has the desired effect.
(3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence
of commands:
(3) The variable may be evaluated incorrectly and LAMMPS may have no
way to detect this has occurred. Consider the following sequence of
commands:
pair_coeff 1 1 1.0 1.0
run 1000