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update fix rigid documentation

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This commit is contained in:
Axel Kohlmeyer
2017-10-20 14:18:50 -04:00
parent 961b976374
commit 83c7d3a1d2
1 changed files with 28 additions and 6 deletions
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34
doc/src/fix_rigid.txt
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@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
{custom} args = {i_propname} or {v_varname}
i_propname = an integer property defined via fix property/atom
v_varname = an atom-style or atomfile-style variable
{group} args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs :pre
@ -80,6 +83,16 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
fix 1 clump rigid custom v_bodyid :pre
variable bodyid atomfile bodies.txt
fix 1 clump rigid custom v_bodyid :pre
fix 0 all property/atom i_bodyid
read_restart data.rigid fix 0 NULL Bodies
fix 1 clump rigid/small custom i_bodyid :pre
[Description:]
@ -100,7 +113,7 @@ of a biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those
modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consiting of one or more point
granular particles, lipid molecules consisting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
@ -203,11 +216,11 @@ most one rigid body. Which atoms are in which bodies can be defined
via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule}, you can define a system that has no rigid
bodies initially. This is useful when you are using the {mol} keyword
in conjunction with another fix that is adding rigid bodies on-the-fly
as molecules, such as "fix deposit"_fix_deposit.html or "fix
pour"_fix_pour.html.
specified as {molecule} or {custom}, you can define a system that has
no rigid bodies initially. This is useful when you are using the {mol}
keyword in conjunction with another fix that is adding rigid bodies
on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
"fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
want. Thus you should be careful to use a fix group that only
includes atoms you want to be part of rigid bodies.
Bodystyle {custom} is similar to bodystyle {molecule}, however some
custom properties are used to group atoms into rigid bodies. The
special case for molecule/body ID = 0 is not available. Possible
custom properties are an integer property associated with atoms through
"fix property/atom"_fix_property_atom.html or an atom style variable
or an atomfile style variable. For the latter two, the variable value
will be rounded to an integer and then rigid bodies defined from
those values.
For bodystyle {group}, each of the listed groups is treated as a
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body. This option is only allowed for the