git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2945 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_modify.html

@@ -45,7 +45,10 @@ subtracted (typically from 3N) as a normalizing factor in a
 temperature computation.  Only computes that compute a temperature use
 this option.  The default is 2 or 3 for <A HREF = "dimension.html">2d or 3d
 systems</A> which is a correction factor for an ensemble
-of velocities with zero total linear momentum.
+of velocities with zero total linear momentum.  You can use a negative
+number for the <I>extra</I> parameter if you need to add
+degrees-of-freedom.  See the <A HREF = "compute_temp_aspher.html">compute
+temp/asphere</A> command for an example.
 </P>
 <P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
 compute group is re-computed each time a temperature is computed.

doc/compute_modify.txt

@@ -38,7 +38,10 @@ subtracted (typically from 3N) as a normalizing factor in a
 temperature computation.  Only computes that compute a temperature use
 this option.  The default is 2 or 3 for "2d or 3d
 systems"_dimension.html which is a correction factor for an ensemble
-of velocities with zero total linear momentum.
+of velocities with zero total linear momentum.  You can use a negative
+number for the {extra} parameter if you need to add
+degrees-of-freedom.  See the "compute
+temp/asphere"_compute_temp_aspher.html command for an example.
 
 The {dynamic} keyword determines whether the number of atoms N in the
 compute group is re-computed each time a temperature is computed.

doc/compute_temp_asphere.html

@@ -32,16 +32,18 @@ translational and rotational kinetic energy.  This differs from the
 usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
 particles with only translational kinetic energy.
 </P>
-<P>For 3d aspherical particles, each has 6 degrees of freedom (3
-translational, 3 rotational).  For 2d aspherical particles, each has 3
-degrees of freedom (2 translational, 1 rotational).
+<P>Only finite-size particles (aspherical or spherical) can be included
+in the group.  For 3d finite-size particles, each has 6 degrees of
+freedom (3 translational, 3 rotational).  For 2d finite-size
+particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
 </P>
-<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) makes the
-assumption that all aspherical particles in your model will freely
-rotate, sampling all their rotational dof.  It is possible to use a
-combination of interaction potentials and fixes that induce no torque
-or otherwise constrain some of all of your particles so that this is
-not the case.  Then there are less dof and you should use the
+<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size aspherical or spherical particles in your model will
+freely rotate, sampling all their rotational dof.  It is possible to
+use a combination of interaction potentials and fixes that induce no
+torque or otherwise constrain some of all of your particles so that
+this is not the case.  Then there are less dof and you should use the
 <A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
 accordingly.
 </P>

doc/compute_temp_asphere.txt

@@ -29,16 +29,18 @@ translational and rotational kinetic energy.  This differs from the
 usual "compute temp"_compute_temp.html command, which assumes point
 particles with only translational kinetic energy.
 
-For 3d aspherical particles, each has 6 degrees of freedom (3
-translational, 3 rotational).  For 2d aspherical particles, each has 3
-degrees of freedom (2 translational, 1 rotational).
+Only finite-size particles (aspherical or spherical) can be included
+in the group.  For 3d finite-size particles, each has 6 degrees of
+freedom (3 translational, 3 rotational).  For 2d finite-size
+particles, each has 3 degrees of freedom (2 translational, 1
+rotational).
 
-IMPORTANT NOTE: This choice for degrees of freedom (dof) makes the
-assumption that all aspherical particles in your model will freely
-rotate, sampling all their rotational dof.  It is possible to use a
-combination of interaction potentials and fixes that induce no torque
-or otherwise constrain some of all of your particles so that this is
-not the case.  Then there are less dof and you should use the
+IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size aspherical or spherical particles in your model will
+freely rotate, sampling all their rotational dof.  It is possible to
+use a combination of interaction potentials and fixes that induce no
+torque or otherwise constrain some of all of your particles so that
+this is not the case.  Then there are less dof and you should use the
 "compute_modify extra"_compute_modify.html command to adjust the dof
 accordingly.
 

doc/compute_temp_sphere.html

@@ -32,13 +32,15 @@ translational and rotational kinetic energy.  This differs from the
 usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
 particles with only translational kinetic energy.
 </P>
-<P>For 3d spherical particles, each has 6 degrees of freedom (3
-translational, 3 rotational).  For 2d spherical particles, each has 3
-degrees of freedom (2 translational, 1 rotational).
+<P>Both point and finite-size particles can be included in the group.
+Point particles do not rotate, so they have only translational degrees
+of freedom.  For 3d spherical particles, each has 6 degrees of freedom
+(3 translational, 3 rotational).  For 2d spherical particles, each has
+3 degrees of freedom (2 translational, 1 rotational).
 </P>
-<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) makes the
-assumption that all spherical particles in your model will freely
-rotate, sampling all their rotational dof.  It is possible to use a
+<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size spherical particles in your model will freely rotate,
+sampling all their rotational dof.  It is possible to use a
 combination of interaction potentials and fixes that induce no torque
 or otherwise constrain some of all of your particles so that this is
 not the case.  Then there are less dof and you should use the
@@ -56,7 +58,7 @@ same as in 3d.
 </P>
 <P>A 6-component kinetic energy tensor is also calculated by this
 compute.  The formula for the components of the tensor is the same as
-the above formula, except that v^2 and w^2 are replaced by vx*vy and
+the above formulas, except that v^2 and w^2 are replaced by vx*vy and
 wx*wy for the xy component.
 </P>
 <P>The number of atoms contributing to the temperature is assumed to be

doc/compute_temp_sphere.txt

@@ -29,13 +29,15 @@ translational and rotational kinetic energy.  This differs from the
 usual "compute temp"_compute_temp.html command, which assumes point
 particles with only translational kinetic energy.
 
-For 3d spherical particles, each has 6 degrees of freedom (3
-translational, 3 rotational).  For 2d spherical particles, each has 3
-degrees of freedom (2 translational, 1 rotational).
+Both point and finite-size particles can be included in the group.
+Point particles do not rotate, so they have only translational degrees
+of freedom.  For 3d spherical particles, each has 6 degrees of freedom
+(3 translational, 3 rotational).  For 2d spherical particles, each has
+3 degrees of freedom (2 translational, 1 rotational).
 
-IMPORTANT NOTE: This choice for degrees of freedom (dof) makes the
-assumption that all spherical particles in your model will freely
-rotate, sampling all their rotational dof.  It is possible to use a
+IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
+all finite-size spherical particles in your model will freely rotate,
+sampling all their rotational dof.  It is possible to use a
 combination of interaction potentials and fixes that induce no torque
 or otherwise constrain some of all of your particles so that this is
 not the case.  Then there are less dof and you should use the
@@ -53,7 +55,7 @@ same as in 3d.
 
 A 6-component kinetic energy tensor is also calculated by this
 compute.  The formula for the components of the tensor is the same as
-the above formula, except that v^2 and w^2 are replaced by vx*vy and
+the above formulas, except that v^2 and w^2 are replaced by vx*vy and
 wx*wy for the xy component.
 
 The number of atoms contributing to the temperature is assumed to be

doc/fix_rigid.html

@@ -156,31 +156,38 @@ 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>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, 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>This fix uses constant-energy NVE-style 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, 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>If you calculate a temperature for the rigid bodies, the
+<P>If you calculate a temperature for particles in 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.
+group includes all the particles in a particular rigid body.
 </P>
-<P>IMPORTANT NOTE: Linear rigid bodies are ones consisting of point
-particles in a straight line.  Linear rigid bodies in 3d with three or
-more atoms also have 5 degrees of freedom instead of 6, but LAMMPS
-will not detect this.  Thus 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>For rigid bodies consisting of point particles, a 3d body has 6
+degrees of freedom (3 translational, 3 rotational), except for a dimer
+which only has 5.  A 2d body has 3 degrees of freedom (2
+translational, 1 rotational).
+</P>
+<P>For rigid bodies containing one or more finite-size particles, a 3d
+body has 6 degrees of freedom, while a 2d body has 3.
+</P>
+<P>IMPORTANT NOTE: A "linear rigid body" is one consisting of 3 or more
+point particles in a straight line.  Linear rigid bodies in 3d have 5
+degrees of freedom (like a dimer) instead of 6, but LAMMPS will not
+detect this.  Thus if your model contains linear rigid bodies you
+should use the <A HREF = "compute_modify.html">compute_modify</A> command to
+subtract an additional degree of freedom for each one.  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.

doc/fix_rigid.txt

@@ -147,31 +147,38 @@ 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.
 
-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, 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.
+This fix uses constant-energy NVE-style 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, 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.
 
-If you calculate a temperature for the rigid bodies, the
+If you calculate a temperature for particles in 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.
+group includes all the particles in a particular rigid body.
 
-IMPORTANT NOTE: Linear rigid bodies are ones consisting of point
-particles in a straight line.  Linear rigid bodies in 3d with three or
-more atoms also have 5 degrees of freedom instead of 6, but LAMMPS
-will not detect this.  Thus 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.
+For rigid bodies consisting of point particles, a 3d body has 6
+degrees of freedom (3 translational, 3 rotational), except for a dimer
+which only has 5.  A 2d body has 3 degrees of freedom (2
+translational, 1 rotational).
+
+For rigid bodies containing one or more finite-size particles, a 3d
+body has 6 degrees of freedom, while a 2d body has 3.
+
+IMPORTANT NOTE: A "linear rigid body" is one consisting of 3 or more
+point particles in a straight line.  Linear rigid bodies in 3d have 5
+degrees of freedom (like a dimer) instead of 6, but LAMMPS will not
+detect this.  Thus if your model contains linear rigid bodies you
+should use the "compute_modify"_compute_modify.html command to
+subtract an additional degree of freedom for each one.  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.