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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8378 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-06-21 23:47:43 +00:00
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40
doc/fix_rigid.html
View File

@ -33,7 +33,7 @@
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>tparam</I> or <I>force</I> or <I>torque</I>
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>tparam</I> or <I>force</I> or <I>torque</I> or <I>infile</I>
<PRE> <I>langevin</I> values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
@ -51,7 +51,9 @@
xflag,yflag,zflag = off/on if component of center-of-mass force is active
<I>torque</I> values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
<I>infile</I> filename
filename = file with per-body values of mass, center-of-mass, moments of inertia
</PRE>
</UL>
@ -255,10 +257,40 @@ rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands.
</P>
<P>The <I>infile</I> keyword allows a file of rigid body attributes to be read
in from a file, rather then letting LAMMPS compute them. There are 3
such attributes: the total mass of the rigid body, its center-of-mass
position, and its 6 moments of inertia. For rigid bodies consisting
of point particles or non-overlapping finite-size particles, LAMMPS
can compute these values accurately. However, for rigid bodies
consisting of finite-size particles which overlap each other, LAMMPS
will ignore the overlaps when computing these 3 attributes. The
amount of error this induces depends on the amount of overlap. To
avoid this issue, the values can be pre-computed (e.g. using Monte
Carlo integration).
</P>
<P>The format of the file is as follows. Note that The file does not
have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain
initial blank lines or comment lines starting with "#" which
are ignored. The first non-blank, non-comment line should
list N = the number of lines to follow. The N successive lines
contain the following information:
</P>
<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
</PRE>
<P>The rigid body IDs are all positive integers. For the <I>single</I>
bodystyle, only an ID of 1 can be used. For the <I>group</I> bodystyle,
IDs from 1 to Ng can be used where Ng is the number of specified
groups. For the <I>molecule</I> bodystyle, use the molecule ID for the
atoms in a specific rigid body as the rigid body ID.
</P>
<HR>
<P>The keyword/value option pairs are used in the following ways.
</P>
<P>If you use a <A HREF = "compute.html">temperature compute</A> with a group that
includes particles in rigid bodies, the degrees-of-freedom removed by
each rigid body are accounted for in the temperature (and pressure)

40
doc/fix_rigid.txt
View File

@ -24,7 +24,7 @@ bodystyle = {single} or {molecule} or {group} :l
groupID1, groupID2, ... = list of N group IDs :pre
zero or more keyword/value pairs may be appended :l
keyword = {langevin} or {temp} or {tparam} or {force} or {torque} :l
keyword = {langevin} or {temp} or {tparam} or {force} or {torque} or {infile} :l
{langevin} values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
@ -41,7 +41,9 @@ keyword = {langevin} or {temp} or {tparam} or {force} or {torque} :l
xflag,yflag,zflag = off/on if component of center-of-mass force is active
{torque} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active :pre
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
{infile} filename
filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
:ule
[Examples:]
@ -244,9 +246,39 @@ rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands.
:line
The {infile} keyword allows a file of rigid body attributes to be read
in from a file, rather then letting LAMMPS compute them. There are 3
such attributes: the total mass of the rigid body, its center-of-mass
position, and its 6 moments of inertia. For rigid bodies consisting
of point particles or non-overlapping finite-size particles, LAMMPS
can compute these values accurately. However, for rigid bodies
consisting of finite-size particles which overlap each other, LAMMPS
will ignore the overlaps when computing these 3 attributes. The
amount of error this induces depends on the amount of overlap. To
avoid this issue, the values can be pre-computed (e.g. using Monte
Carlo integration).
The keyword/value option pairs are used in the following ways.
The format of the file is as follows. Note that The file does not
have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain
initial blank lines or comment lines starting with "#" which
are ignored. The first non-blank, non-comment line should
list N = the number of lines to follow. The N successive lines
contain the following information:
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz :pre
The rigid body IDs are all positive integers. For the {single}
bodystyle, only an ID of 1 can be used. For the {group} bodystyle,
IDs from 1 to Ng can be used where Ng is the number of specified
groups. For the {molecule} bodystyle, use the molecule ID for the
atoms in a specific rigid body as the rigid body ID.
:line
If you use a "temperature compute"_compute.html with a group that
includes particles in rigid bodies, the degrees-of-freedom removed by