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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2657 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-03-17 15:41:12 +00:00
parent 5dc6a9e054
commit dec203161a
8 changed files with 50 additions and 23 deletions
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26
doc/group.html
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@ -17,9 +17,10 @@
</PRE>
<UL><LI>ID = user-defined name of the group
<LI>style = <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>subtract</I> or <I>union</I> or <I>intersect</I>
<PRE> <I>region</I> args = region-ID
<PRE> <I>delete</I> = no args
<I>region</I> args = region-ID
<I>type</I> or <I>id</I> or <I>molecule</I>
args = one or more atom types, atom IDs, or molecule IDs
args = logical value
@ -43,17 +44,27 @@ group sub id <= 150
group polyA molecule <> 50 250
group boundary subtract all a2 a3
group boundary union lower upper
group boundary intersect upper flow
group boundary intersect upper flow
group boundary delete
</PRE>
<P><B>Description:</B>
</P>
<P>Identify a collection of atoms as belonging to a group. The group ID
can then be used in other commands such as fix, velocity, dump, or
temperature to act on the atoms together.
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.
</P>
<P>If the group ID already exists, the group command adds the specified
atoms to the group.
</P>
<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>
<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
@ -85,11 +96,12 @@ 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
group.
group. This group cannot be deleted.
</P>
<P><B>Restrictions:</B>
</P>
<P>There can be no more than 32 defined groups, including "all".
<P>There can be no more than 32 groups defined at one time, including
"all".
</P>
<P><B>Related commands:</B>
</P>

24
doc/group.txt
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@ -13,8 +13,9 @@ group command :h3
group ID style args :pre
ID = user-defined name of the group :ulb,l
style = {region} or {type} or {id} or {molecule} or {subtract} or \
style = {delete} or {region} or {type} or {id} or {molecule} or {subtract} or \
{union} or {intersect} :l
{delete} = no args
{region} args = region-ID
{type} or {id} or {molecule}
args = one or more atom types, atom IDs, or molecule IDs
@ -38,17 +39,27 @@ group sub id <= 150
group polyA molecule <> 50 250
group boundary subtract all a2 a3
group boundary union lower upper
group boundary intersect upper flow :pre
group boundary intersect upper flow
group boundary delete :pre
[Description:]
Identify a collection of atoms as belonging to a group. The group ID
can then be used in other commands such as fix, velocity, dump, or
temperature to act on the atoms together.
can then be used in other commands such as "fix"_fix.html,
"compute"_compute.html, "dump"_dump.html, or "velocity"_velocity.html
to act on those atoms together.
If the group ID already exists, the group command adds the specified
atoms to the group.
The {delete} 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
{delete} 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 "fix"_fix.html or "compute"_compute.html
or "dump"_dump.html.
The {region} 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
@ -80,11 +91,12 @@ as arguments. Atoms that belong to every one of the listed groups are
added to the specified group.
A group with the ID {all} is predefined. All atoms belong to this
group.
group. This group cannot be deleted.
[Restrictions:]
There can be no more than 32 defined groups, including "all".
There can be no more than 32 groups defined at one time, including
"all".
[Related commands:]

5
doc/neigh_modify.html
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@ -42,9 +42,8 @@
<I>page</I> value = N
N = number of pairs stored in a single neighbor page
<I>one</I> value = N
N = max number of neighbors of one atom
</PRE>
<PRE> <I>binsize</I> value = size
N = max number of neighbors of one atom
<I>binsize</I> value = size
size = bin size for neighbor list construction (distance units)
</PRE>

2
doc/neigh_modify.txt
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@ -38,7 +38,7 @@ keyword = {delay} or {every} or {check} or {once} or {include} or {exclude} or {
{page} value = N
N = number of pairs stored in a single neighbor page
{one} value = N
N = max number of neighbors of one atom :pre
N = max number of neighbors of one atom
{binsize} value = size
size = bin size for neighbor list construction (distance units) :pre
:ule

4
doc/thermo_style.html
View File

@ -27,7 +27,8 @@
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
xy, xz, yz,
pxx, pyy, pzz, pxy, pxz, pyz,
c_ID, c_ID[n], f_ID, f_ID[n], v_name
step = timestep
atoms = # of atoms
@ -51,6 +52,7 @@
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
c_ID = global scalar value calculated by a compute with ID
c_ID[N] = Nth component of global vector calculated by a compute with ID

4
doc/thermo_style.txt
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@ -22,7 +22,8 @@ args = list of arguments for a particular style :l
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
xy, xz, yz,
pxx, pyy, pzz, pxy, pxz, pyz,
c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
step = timestep
atoms = # of atoms
@ -46,6 +47,7 @@ args = list of arguments for a particular style :l
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
c_ID = global scalar value calculated by a compute with ID
c_ID\[N\] = Nth component of global vector calculated by a compute with ID

4
doc/variable.html
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@ -118,7 +118,7 @@ for example, in a loop.
<P>Second, as described below, if a variable is iterated on to the end of
its list of strings via the <A HREF = "next.html">next</A> command, it is removed
from the list of active variables, and is thus available to be
re-defined in a subsequent variable command. The <I>delete</I> option does
re-defined in a subsequent variable command. The <I>delete</I> style does
the same thing.
</P>
<HR>
@ -138,7 +138,7 @@ skipped. This enables the construction of simple loops in the input
script that are iterated over and then exited from.
</P>
<P>As explained above, an exhausted variable can be re-used in an input
script. The <I>delete</I> option also removes the variable, the same as if
script. The <I>delete</I> style also removes the variable, the same as if
it were exhausted, allowing it to be redefined later in the input
script or when the input script is looped over. This can be useful
when breaking out of a loop via the <A HREF = "if.html">if</A> and <A HREF = "jump.html">jump</A>

4
doc/variable.txt
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@ -112,7 +112,7 @@ for example, in a loop.
Second, as described below, if a variable is iterated on to the end of
its list of strings via the "next"_next.html command, it is removed
from the list of active variables, and is thus available to be
re-defined in a subsequent variable command. The {delete} option does
re-defined in a subsequent variable command. The {delete} style does
the same thing.
:line
@ -132,7 +132,7 @@ skipped. This enables the construction of simple loops in the input
script that are iterated over and then exited from.
As explained above, an exhausted variable can be re-used in an input
script. The {delete} option also removes the variable, the same as if
script. The {delete} style also removes the variable, the same as if
it were exhausted, allowing it to be redefined later in the input
script or when the input script is looped over. This can be useful
when breaking out of a loop via the "if"_if.html and "jump"_jump.html