langevin 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
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
+ 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
@@ -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.
+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 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 ++
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. +
The keyword/value option pairs are used in the following ways. -
If you use a temperature compute 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) diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 3d49aedd6d..c19145a825 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -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