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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5654 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-02-15 21:14:11 +00:00
parent 7814f1cc56
commit eaa65992c5
6 changed files with 56 additions and 30 deletions
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7
doc/fix_orient_fcc.html
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@ -126,11 +126,16 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<P>This fix calculates a global scalar which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The scalar is the
potential energy change due to this fix. The scalar value calculated
by this fix is "extensive".
</P>
<P>This fix also calculates a per-atom array which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The array stores
the order parameter Xi and normalized order parameter (0 to 1) for
each atom. The per-atom values can be accessed on any timestep.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.

7
doc/fix_orient_fcc.txt
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@ -123,11 +123,16 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
This fix calculates a global scalar which can be accessed by various
"output commands"_Section_howto.html#4_15. The scalar is the
potential energy change due to this fix. The scalar value calculated
by this fix is "extensive".
This fix also calculates a per-atom array which can be accessed by
various "output commands"_Section_howto.html#4_15. The array stores
the order parameter Xi and normalized order parameter (0 to 1) for
each atom. The per-atom values can be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.

19
doc/fix_rigid.html
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@ -148,6 +148,18 @@ different molecule ID is treated as a rigid body.
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body.
</P>
<P>IMPORTANT NOTE: To compute the initial center-of-mass position and
other properties of each rigid body, the image flags for each atom in
the body are used to "unwrap" the atom coordinates. Thus you must
insure that these image flags are consistent so that the unwrapping
creates a valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
<A HREF = "set.html">set</A> command to specify them correctly. If a dimension is
non-periodic then the image flag of each atom must be 0 in that
dimension, else an error is generated.
</P>
<P>By default, each rigid body is acted on by other atoms which induce an
external force and torque on its center of mass, causing it to
translate and rotate. Components of the external center-of-mass force
@ -285,7 +297,7 @@ cumulative energy change due to the thermostatting the fix performs.
<P>All of these fixes compute a global array of values which can be
accessed by various <A HREF = "Section_howto.html#4_15">output commands</A>. The
number of rows in the array is equal to the number of rigid bodies.
The number of columns is 15. Thus for each rigid body, 12 values are
The number of columns is 15. Thus for each rigid body, 15 values are
stored: the xyz coords of the center of mass (COM), the xyz components
of the COM velocity, the xyz components of the force acting on the
COM, the xyz components of the torque acting on the COM, and the xyz
@ -315,11 +327,6 @@ proportional in length to the number of rigid bodies. Hence they will
not scale well in parallel if large numbers of rigid bodies are
simulated.
</P>
<P>If the atoms in a single rigid body initially straddle a periodic
boundary, the input data file must define the image flags for each
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
rigid body.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "neigh_modify.html">neigh_modify</A>

19
doc/fix_rigid.txt
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@ -137,6 +137,18 @@ For bodystyle {group}, each of the listed groups is treated as a
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body.
IMPORTANT NOTE: To compute the initial center-of-mass position and
other properties of each rigid body, the image flags for each atom in
the body are used to "unwrap" the atom coordinates. Thus you must
insure that these image flags are consistent so that the unwrapping
creates a valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
"set"_set.html command to specify them correctly. If a dimension is
non-periodic then the image flag of each atom must be 0 in that
dimension, else an error is generated.
By default, each rigid body is acted on by other atoms which induce an
external force and torque on its center of mass, causing it to
translate and rotate. Components of the external center-of-mass force
@ -274,7 +286,7 @@ cumulative energy change due to the thermostatting the fix performs.
All of these fixes compute a global array of values which can be
accessed by various "output commands"_Section_howto.html#4_15. The
number of rows in the array is equal to the number of rigid bodies.
The number of columns is 15. Thus for each rigid body, 12 values are
The number of columns is 15. Thus for each rigid body, 15 values are
stored: the xyz coords of the center of mass (COM), the xyz components
of the COM velocity, the xyz components of the force acting on the
COM, the xyz components of the torque acting on the COM, and the xyz
@ -304,11 +316,6 @@ proportional in length to the number of rigid bodies. Hence they will
not scale well in parallel if large numbers of rigid bodies are
simulated.
If the atoms in a single rigid body initially straddle a periodic
boundary, the input data file must define the image flags for each
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
rigid body.
[Related commands:]
"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html

17
doc/set.html
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@ -156,14 +156,15 @@ PeriDynamics), then it also sets their mass.
by PeriDynamics.
</P>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An
image of 0 means it is inside the box as defined. A value of 2 means
add 2 box lengths to get the true value. A value of -1 means subtract
1 box length to get the true value. LAMMPS updates these flags as
atoms cross periodic boundaries during the simulation. The flags can
be output with atom snapshots via the <A HREF = "dump.html">dump</A> command. If a
value of NULL is specified for any of nx,ny,nz, then the current image
value for that dimension is unchanged.
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
<A HREF = "dump.html">dump</A> command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 is allowed
to be specified.
</P>
<P>This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.

17
doc/set.txt
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@ -150,14 +150,15 @@ Keyword {volume} sets the volume of all selected particles, as defined
by PeriDynamics.
Keyword {image} sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An
image of 0 means it is inside the box as defined. A value of 2 means
add 2 box lengths to get the true value. A value of -1 means subtract
1 box length to get the true value. LAMMPS updates these flags as
atoms cross periodic boundaries during the simulation. The flags can
be output with atom snapshots via the "dump"_dump.html command. If a
value of NULL is specified for any of nx,ny,nz, then the current image
value for that dimension is unchanged.
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
"dump"_dump.html command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 is allowed
to be specified.
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.