ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
This commit is contained in:
sjplimp
2009-01-22 18:56:18 +00:00
parent 4eeb3d4397
commit 486aa1a7f5
2 changed files with 40 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

37
doc/fix_rigid.html
View File

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