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doc/Section_commands.html
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@ -346,11 +346,11 @@ of each style or click on the style itself for a full description:
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -464,6 +464,7 @@ each style or click on the style itself for a full description:
"centro/atom"_compute_centro_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"displace/atom"_compute_displace_atom.html,

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doc/compute.html
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@ -111,6 +111,7 @@ available in LAMMPS:
</P>
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom

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doc/compute.txt
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@ -108,6 +108,7 @@ available in LAMMPS:
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"com"_compute_com.html - center-of-mass of group of atoms
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
"displace/atom"_compute_displace_atom.html - displacement of each atom

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@ -0,0 +1,67 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute com command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID com
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>com = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all com
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.
</P>
<P>A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
center-of-mass 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>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 its contribution to the center-of-mass may not reflect its true
contribution. See the <A HREF = "fix_rigid.html">fix rigid</A> command for details.
Thus, to compute the center-of-mass 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><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector 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>The vector values are "intensive", meaning they are independent of the
number of atoms in the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute com command :h3
[Syntax:]
compute ID group-ID com :pre
ID, group-ID are documented in "compute"_compute.html command
com = style name of this compute command :ul
[Examples:]
compute 1 all com :pre
[Description:]
Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.
A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
IMPORTANT NOTE: The coordinates of an atom contribute to the
center-of-mass 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
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and its contribution to the center-of-mass may not reflect its true
contribution. See the "fix rigid"_fix_rigid.html command for details.
Thus, to compute the center-of-mass 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.
[Output info:]
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
The vector values are "intensive", meaning they are independent of the
number of atoms in the simulation.
[Restrictions:] none
[Related commands:] none
[Default:] none

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@ -59,7 +59,7 @@ 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 displacement will not reflect its true displacement.
and the computed displacement may 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>

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doc/compute_displace_atom.txt
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@ -56,7 +56,7 @@ 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 displacement will not reflect its true displacement.
and the computed displacement may 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

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@ -29,8 +29,8 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all compute
fix 1 upper compute com yes
<PRE>compute 1 all msd
compute 1 upper msd com yes
</PRE>
<P><B>Description:</B>
</P>
@ -44,8 +44,8 @@ and averaged over atoms in the group. The 4th component is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.
</P>
<P>The slope of the mean-squared displacement versus time is proportional
to the diffusion coefficient of the diffusing atoms.
<P>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
@ -75,11 +75,11 @@ 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 its contribution to the MSD may not reflect its true contribution.
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.
</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>,

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doc/compute_msd.txt
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@ -21,8 +21,8 @@ keyword = {com} :l
[Examples:]
fix 1 all compute
fix 1 upper compute com yes :pre
compute 1 all msd
compute 1 upper msd com yes :pre
[Description:]
@ -36,8 +36,8 @@ and averaged over atoms in the group. The 4th component is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.
The slope of the mean-squared displacement versus time is proportional
to the diffusion coefficient of the diffusing atoms.
The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
@ -67,11 +67,11 @@ 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 its contribution to the MSD may not reflect its true contribution.
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.
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,