From 83c7d3a1d2e64ef5dfa14515ac6c596b1ad7627e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 20 Oct 2017 14:18:50 -0400 Subject: [PATCH] update fix rigid documentation --- doc/src/fix_rigid.txt | 34 ++++++++++++++++++++++++++++------ 1 file changed, 28 insertions(+), 6 deletions(-) diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 99105e1350..a5a631bd38 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -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