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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1364 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-01-09 23:22:14 +00:00
parent 1e62548d71
commit 616ad71c82
2 changed files with 30 additions and 34 deletions
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32
doc/fix_rigid.html
View File

@ -68,24 +68,22 @@ to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and
includes all the desired rigid bodies. LAMMPS will allow multiple
rigid fixes to be defined, but it is more expensive.
</P>
<P>The degrees-of-freedom removed by rigid bodies are accounted for in
temperature and pressure computations. Similary, the rigid body
contribution to the pressure virial is also accounted for. The latter
is only correct if forces within the bodies have been turned off, and
there is only a single fix rigid defined. For each linear rigid body
of three or more atoms, one degree-of-freedom must be subtracted using
a <A HREF = "compute_modify.html">compute_modify</A> command (i.e. 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).
<P>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 <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.
</P>
<P>Note that 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 <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.
<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.
</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

32
doc/fix_rigid.txt
View File

@ -61,24 +61,22 @@ For computational efficiency, you should define one fix rigid which
includes all the desired rigid bodies. LAMMPS will allow multiple
rigid fixes to be defined, but it is more expensive.
The degrees-of-freedom removed by rigid bodies are accounted for in
temperature and pressure computations. Similary, the rigid body
contribution to the pressure virial is also accounted for. The latter
is only correct if forces within the bodies have been turned off, and
there is only a single fix rigid defined. For each linear rigid body
of three or more atoms, one degree-of-freedom must be subtracted using
a "compute_modify"_compute_modify.html command (i.e. 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).
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.
Note that 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.
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.
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