From 486aa1a7f54d60d5557ef068a624ec36e4860bea Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Jan 2009 18:56:18 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2518 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_rigid.html | 37 ++++++++++++++++++++----------------- doc/fix_rigid.txt | 37 ++++++++++++++++++++----------------- 2 files changed, 40 insertions(+), 34 deletions(-) diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index a1d380cf76..814f513ed9 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -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 fix langevin 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 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 -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 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 diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 58d567f146..f7acb62250 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -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