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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3499 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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18
doc/Section_howto.html
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@ -986,15 +986,15 @@ be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A>
output. Each of these are described in turn.
</P>
<P>In LAMMPS, a <A HREF = "compute.html">compute</A> comes in two flavors: ones that
compute global values (e.g. temperature, pressure tensor) and ones
that compute per-atom values. Only global quantities from a compute
can be used for thermodynamic output. The user-defined ID of the
compute is used along with an optional subscript as part of the
<A HREF = "thermo_style.html">thermo_style</A> command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp[2] outputs
the 2nd vector value. Note that there is a <A HREF = "compute_reduce.html">compute
reduce</A> command which can sum per-atom quantities
into a global scalar or vector.
compute global values (a scalar or a vector, e.g. temperature,
6-element pressure tensor) and ones that compute per-atom values.
Only global quantities from a compute can be used for thermodynamic
output. The user-defined ID of the compute is used along with an
optional subscript as part of the <A HREF = "thermo_style.html">thermo_style</A>
command. E.g. c_myTemp outputs the single scalar value generated by
the compute; c_myTemp[2] outputs the 2nd vector value. Note that
there is a <A HREF = "compute_reduce.html">compute reduce</A> command which can sum
per-atom quantities into a global scalar or vector.
</P>
<P><A HREF = "fix.html">Fixes</A> can generate global scalar or vector values which can
be output with thermodynamic output, e.g. the energy of an indenter's

18
doc/Section_howto.txt
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@ -979,15 +979,15 @@ be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or
output. Each of these are described in turn.
In LAMMPS, a "compute"_compute.html comes in two flavors: ones that
compute global values (e.g. temperature, pressure tensor) and ones
that compute per-atom values. Only global quantities from a compute
can be used for thermodynamic output. The user-defined ID of the
compute is used along with an optional subscript as part of the
"thermo_style"_thermo_style.html command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp\[2\] outputs
the 2nd vector value. Note that there is a "compute
reduce"_compute_reduce.html command which can sum per-atom quantities
into a global scalar or vector.
compute global values (a scalar or a vector, e.g. temperature,
6-element pressure tensor) and ones that compute per-atom values.
Only global quantities from a compute can be used for thermodynamic
output. The user-defined ID of the compute is used along with an
optional subscript as part of the "thermo_style"_thermo_style.html
command. E.g. c_myTemp outputs the single scalar value generated by
the compute; c_myTemp\[2\] outputs the 2nd vector value. Note that
there is a "compute reduce"_compute_reduce.html command which can sum
per-atom quantities into a global scalar or vector.
"Fixes"_fix.html can generate global scalar or vector values which can
be output with thermodynamic output, e.g. the energy of an indenter's

23
doc/compute_displace_atom.html
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@ -28,12 +28,13 @@
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.
</P>
<P>A vector of four quantites per atom are calculated by this compute.
The first 3 elements of the cector are the dx,dy,dz displacements.
<P>A vector of four quantites per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).
</P>
<P>To store the original coordinates at the time this compute is issued,
<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 creates its own fix of style "coord/original", as if this
command had been issued:
</P>
@ -58,11 +59,11 @@ image</A> command.
</P>
<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,
and the computed MSD will not reflect its true displacement. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the
atoms in the bodies.
and the computed displacement will not reflect its true displacement.
See the <A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to
compute the displacement of rigid bodies as they cross periodic
boundaries, you will need to post-process a <A HREF = "dump.html">dump file</A>
containing coordinates of the atoms in the bodies.
</P>
<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
@ -74,9 +75,9 @@ file.
<P><B>Output info:</B>
</P>
<P>This compute calculates a vector of length 4 for each atom, which can
be accessed by indices 1-4 by any command that uses per-atom computes
as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview
of LAMMPS output options.
be accessed by indices 1-4 by any command that uses per-atom values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

23
doc/compute_displace_atom.txt
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@ -25,12 +25,13 @@ Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.
A vector of four quantites per atom are calculated by this compute.
The first 3 elements of the cector are the dx,dy,dz displacements.
A vector of four quantites per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).
To store the original coordinates at the time this compute is issued,
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 creates its own fix of style "coord/original", as if this
command had been issued:
@ -55,11 +56,11 @@ image"_set.html command.
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,
and the computed MSD will not reflect its true displacement. See the
"fix rigid"_fix_rigid.html command for details. Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a "dump file"_dump.html containing coordinates of the
atoms in the bodies.
and the computed displacement will not reflect its true displacement.
See the "fix rigid"_fix_rigid.html command for details. Thus, to
compute the displacement of rigid bodies as they cross periodic
boundaries, you will need to post-process a "dump file"_dump.html
containing coordinates of the atoms in the bodies.
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,
@ -71,9 +72,9 @@ file.
[Output info:]
This compute calculates a vector of length 4 for each atom, which can
be accessed by indices 1-4 by any command that uses per-atom computes
as input. See "this section"_Section_howto.html#4_15 for an overview
of LAMMPS output options.
be accessed by indices 1-4 by any command that uses per-atom values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
[Restrictions:] none