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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10001 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-05-31 16:50:53 +00:00
parent 4065c19102
commit 4205e9c9d3
4 changed files with 48 additions and 86 deletions
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30
doc/compute_displace_atom.html
View File

@ -34,28 +34,16 @@ The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz). dz*dz).
</P> </P>
<P>The displacement of an atom is from its original position at the time <P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates, the compute command was issued. The value of the displacement will be
the compute creates its own fix of style "store/state", as if this 0.0 for atoms not in the specified compute group.
command had been issued:
</P> </P>
<PRE>fix compute-ID_store_state group-ID store/state xu yu zu <P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
</PRE> using the image flags associated with each atom. See the <A HREF = "dump.html">dump
<P>See the <A HREF = "fix_store_state.html">fix store/state</A> command for details. custom</A> command for a discussion of "unwrapped" coordinates.
Note that the ID of the new fix is the compute-ID + underscore + See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
"store/state", and the group for the new fix is the same as the discussion of image flags and how they are set for each atom. You can
compute group. reset the image flags (e.g. to 0) before invoking this compute by
</P> using the <A HREF = "set.html">set image</A> command.
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
</P>
<P>IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P> </P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix <P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered, rigid</A> command), it's periodic image flags are altered,

30
doc/compute_displace_atom.txt
View File

@ -31,28 +31,16 @@ The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz). dz*dz).
The displacement of an atom is from its original position at the time The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates, the compute command was issued. The value of the displacement will be
the compute creates its own fix of style "store/state", as if this 0.0 for atoms not in the specified compute group.
command had been issued:
fix compute-ID_store_state group-ID store/state xu yu zu :pre IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the "dump
See the "fix store/state"_fix_store_state.html command for details. custom"_dump.html command for a discussion of "unwrapped" coordinates.
Note that the ID of the new fix is the compute-ID + underscore + See the Atoms section of the "read_data"_read_data.html command for a
"store/state", and the group for the new fix is the same as the discussion of image flags and how they are set for each atom. You can
compute group. reset the image flags (e.g. to 0) before invoking this compute by
using the "set image"_set.html command.
The value of the displacement will be 0.0 for atoms not in the
specified compute group.
IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
"read_data"_read_data.html command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set
image"_set.html command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered, rigid"_fix_rigid.html command), it's periodic image flags are altered,

37
doc/compute_msd.html
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@ -36,7 +36,9 @@ compute 1 upper msd com yes
</P> </P>
<P>Define a computation that calculates the mean-squared displacement <P>Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms (MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries. passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the <A HREF = "compute_msd_nongauss.html">compute
msd/nongauss</A> command.
</P> </P>
<P>A vector of four quantites is calculated by this compute. The first 3 <P>A vector of four quantites is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed elements of the vector are the squared dx,dy,dz displacements, summed
@ -48,30 +50,20 @@ averaged over atoms in the group.
proportional to the diffusion coefficient of the diffusing atoms. proportional to the diffusion coefficient of the diffusing atoms.
</P> </P>
<P>The displacement of an atom is from its original position at the time <P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates, the compute command was issued. The value of the displacement will be
the compute creates its own fix of style "store/state", as if this 0.0 for atoms not in the specified compute group.
command had been issued:
</P>
<PRE>fix compute-ID_store_state group-ID store/state xu yu zu
</PRE>
<P>See the <A HREF = "fix_store_state.html">fix store/state</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_state", and the group for the new fix is the same as the
compute group.
</P> </P>
<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in <P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated. The <I>com</I> option is also displacment of each atom is calcluated.
passed to the created fix store/state.
</P> </P>
<P>IMPORTANT NOTE: Fix store/state stores the initial coordinates in <P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
"unwrapped" form, by using the image flags associated with each atom. using the image flags associated with each atom. See the <A HREF = "dump.html">dump
See the <A HREF = "dump.html">dump custom</A> command for a discussion of custom</A> command for a discussion of "unwrapped" coordinates.
"unwrapped" coordinates. See the Atoms section of the See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and discussion of image flags and how they are set for each atom. You can
how they are set for each atom. You can reset the image flags reset the image flags (e.g. to 0) before invoking this compute by
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set using the <A HREF = "set.html">set image</A> command.
image</A> command.
</P> </P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix <P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered, rigid</A> command), it's periodic image flags are altered,
@ -103,7 +95,8 @@ distance^2 <A HREF = "units.html">units</A>.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store_state.html">fix <P><A HREF = "compute_msd_nongauss.html">compute msd/nongauss</A>, <A HREF = "compute_displace_atom.html">compute
displace_atom</A>, <A HREF = "fix_store_state.html">fix
store/state</A>, <A HREF = "compute_msd_molecule.html">compute store/state</A>, <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A> msd/molecule</A>
</P> </P>

37
doc/compute_msd.txt
View File

@ -28,7 +28,9 @@ compute 1 upper msd com yes :pre
Define a computation that calculates the mean-squared displacement Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms (MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries. passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the "compute
msd/nongauss"_compute_msd_nongauss.html command.
A vector of four quantites is calculated by this compute. The first 3 A vector of four quantites is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed elements of the vector are the squared dx,dy,dz displacements, summed
@ -40,30 +42,20 @@ The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms. proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates, the compute command was issued. The value of the displacement will be
the compute creates its own fix of style "store/state", as if this 0.0 for atoms not in the specified compute group.
command had been issued:
fix compute-ID_store_state group-ID store/state xu yu zu :pre
See the "fix store/state"_fix_store_state.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_state", and the group for the new fix is the same as the
compute group.
If the {com} option is set to {yes} then the effect of any drift in If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated. The {com} option is also displacment of each atom is calcluated.
passed to the created fix store/state.
IMPORTANT NOTE: Fix store/state stores the initial coordinates in IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
"unwrapped" form, by using the image flags associated with each atom. using the image flags associated with each atom. See the "dump
See the "dump custom"_dump.html command for a discussion of custom"_dump.html command for a discussion of "unwrapped" coordinates.
"unwrapped" coordinates. See the Atoms section of the See the Atoms section of the "read_data"_read_data.html command for a
"read_data"_read_data.html command for a discussion of image flags and discussion of image flags and how they are set for each atom. You can
how they are set for each atom. You can reset the image flags reset the image flags (e.g. to 0) before invoking this compute by
(e.g. to 0) before invoking this compute by using the "set using the "set image"_set.html command.
image"_set.html command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered, rigid"_fix_rigid.html command), it's periodic image flags are altered,
@ -95,7 +87,8 @@ distance^2 "units"_units.html.
[Related commands:] [Related commands:]
"compute displace_atom"_compute_displace_atom.html, "fix "compute msd/nongauss"_compute_msd_nongauss.html, "compute
displace_atom"_compute_displace_atom.html, "fix
store/state"_fix_store_state.html, "compute store/state"_fix_store_state.html, "compute
msd/molecule"_compute_msd_molecule.html msd/molecule"_compute_msd_molecule.html