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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2518 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-01-22 18:56:18 +00:00
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37
doc/fix_rigid.html
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@ -115,24 +115,27 @@ rigid fixes to be defined, but it is more expensive.
additional constraints to control the temperature of an ensemble of
rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this
purpose to treat the system as effectively immersed in an implicit
solvent, i.e. a Brownian dynamics model. Or you can thermostat
additional atoms of an explicit solvent directly.
solvent, e.g. a Brownian dynamics model. Or you can thermostat only
the non-rigid atoms that surround one or more rigid bodies
(i.e. explicit solvent) by appropriate choice of groups in the compute
and fix commands for temperature and thermostatting.
</P>
<P>The degrees-of-freedom removed by rigid bodies are accounted for in
temperature and pressure computations. Similarly, the rigid body
contribution to the pressure of the system (virial) is also accounted
for. For linear rigid bodies of three or more atoms, one additional
degree-of-freedom must be subtracted manually using the
<A HREF = "compute_modify.html">compute_modify</A> command. E.g. for a simulation
of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
after the thermo_style command, where 3 is the default setting and an
additional 10 degrees-of-freedom are subtracted. You may also wish to
manually subtract additional degrees-of-freedom if you use the <I>force</I>
and <I>torque</I> keywords to eliminate certain motions of the rigid body.
Alternatively, you can define the temperature <A HREF = "compute.html">compute</A>
to exclude atoms in rigid bodies, which may be a better strategy,
i.e. measure the temperature of the free atoms around the rigid body
or bodies.
<P>If you do calculate a temperature for the rigid bodies, the
degrees-of-freedom removed by each rigid body are accounted for in the
temperature (and pressure) computation, but only if the temperature
group includes the entire rigid body. Rigid bodies in 3d have 6
degrees of freedom (3 translational, 3 rotational), except for dimers
which only have 5. Rigid bodies in 2d have 3 degrees of freedom.
Note that linear rigid bodies in 3d of three or more atoms also have 5
degrees of freedom instead of 6, but LAMMPS will not detect this. So
you should use the <A HREF = "compute_modify.html">compute_modify</A> command to
subtract an additional degree of freedom per rigid body. You may also
wish to explicitly subtract additional degrees-of-freedom if you use
the <I>force</I> and <I>torque</I> keywords to eliminate certain motions of the
rigid body, as LAMMPS does not do this automatically.
</P>
<P>The rigid body contribution to the pressure of the system (virial) is
also accounted for by this fix.
</P>
<P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a

37
doc/fix_rigid.txt
View File

@ -106,24 +106,27 @@ This fix uses constant-energy integration, so you may need to impose
additional constraints to control the temperature of an ensemble of
rigid bodies. You can use "fix langevin"_fix_langevin.html for this
purpose to treat the system as effectively immersed in an implicit
solvent, i.e. a Brownian dynamics model. Or you can thermostat
additional atoms of an explicit solvent directly.
solvent, e.g. a Brownian dynamics model. Or you can thermostat only
the non-rigid atoms that surround one or more rigid bodies
(i.e. explicit solvent) by appropriate choice of groups in the compute
and fix commands for temperature and thermostatting.
The degrees-of-freedom removed by rigid bodies are accounted for in
temperature and pressure computations. Similarly, the rigid body
contribution to the pressure of the system (virial) is also accounted
for. For linear rigid bodies of three or more atoms, one additional
degree-of-freedom must be subtracted manually using the
"compute_modify"_compute_modify.html command. E.g. for a simulation
of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
after the thermo_style command, where 3 is the default setting and an
additional 10 degrees-of-freedom are subtracted. You may also wish to
manually subtract additional degrees-of-freedom if you use the {force}
and {torque} keywords to eliminate certain motions of the rigid body.
Alternatively, you can define the temperature "compute"_compute.html
to exclude atoms in rigid bodies, which may be a better strategy,
i.e. measure the temperature of the free atoms around the rigid body
or bodies.
If you do calculate a temperature for the rigid bodies, the
degrees-of-freedom removed by each rigid body are accounted for in the
temperature (and pressure) computation, but only if the temperature
group includes the entire rigid body. Rigid bodies in 3d have 6
degrees of freedom (3 translational, 3 rotational), except for dimers
which only have 5. Rigid bodies in 2d have 3 degrees of freedom.
Note that linear rigid bodies in 3d of three or more atoms also have 5
degrees of freedom instead of 6, but LAMMPS will not detect this. So
you should use the "compute_modify"_compute_modify.html command to
subtract an additional degree of freedom per rigid body. You may also
wish to explicitly subtract additional degrees-of-freedom if you use
the {force} and {torque} keywords to eliminate certain motions of the
rigid body, as LAMMPS does not do this automatically.
The rigid body contribution to the pressure of the system (virial) is
also accounted for by this fix.
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a