ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update fix rigid documentation

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

34
doc/src/fix_rigid.txt
View File

@ -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 bodystyle = {single} or {molecule} or {group} :l
{single} args = none {single} args = none
{molecule} 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 ... {group} args = N groupID1 groupID2 ...
N = # of groups N = # of groups
groupID1, groupID2, ... = list of N group IDs :pre groupID1, groupID2, ... = list of N group IDs :pre
@ -81,6 +84,16 @@ 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
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0 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 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:] [Description:]
Treat one or more sets of atoms as independent rigid bodies. This Treat one or more sets of atoms as independent rigid bodies. This
@ -100,7 +113,7 @@ of a biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those Example of small rigid bodies are patchy nanoparticles, such as those
modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of 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 dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a 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. via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule}, you can define a system that has no rigid specified as {molecule} or {custom}, you can define a system that has
bodies initially. This is useful when you are using the {mol} keyword no rigid bodies initially. This is useful when you are using the {mol}
in conjunction with another fix that is adding rigid bodies on-the-fly keyword in conjunction with another fix that is adding rigid bodies
as molecules, such as "fix deposit"_fix_deposit.html or "fix on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
pour"_fix_pour.html. "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles. 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 want. Thus you should be careful to use a fix group that only
includes atoms you want to be part of rigid bodies. 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 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 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 included in each rigid body. This option is only allowed for the