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sjplimp 2011-03-08 22:23:59 +00:00
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16
doc/Section_commands.html
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@ -364,14 +364,14 @@ 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_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_com_molecule.html">com/molecule</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_dihedral_local.html">dihedral/local</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_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pair_local.html">pair/local</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_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><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></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A>
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</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_dihedral_local.html">dihedral/local</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_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</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_property_atom.html">property/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_ti.html">ti</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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@ -503,6 +503,7 @@ each style or click on the style itself for a full description:
"atom/molecule"_compute_atom_molecule.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/molecule"_compute_com_molecule.html,

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doc/compute.html
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@ -171,6 +171,7 @@ available in LAMMPS:
<LI><A HREF = "compute_atom_molecule.html">atom/molecule</A> - sum per-atom properties for each molecule
<LI><A HREF = "compute_bond_local.html">bond/local</A> - distance and energy of each bond
<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_cluster_atom.html">cluster/atom</A> - cluster ID 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_com_molecule.html">com/molecule</A> - center-of-mass for each molecule

1
doc/compute.txt
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@ -166,6 +166,7 @@ available in LAMMPS:
"atom/molecule"_compute_atom_molecule.html - sum per-atom properties for each molecule
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"cluster/atom"_compute_cluster_atom.html - cluster ID 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
"com/molecule"_compute_com_molecule.html - center-of-mass for each molecule

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@ -0,0 +1,62 @@
<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 cluster/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID cluster/atom cutoff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>cluster/atom = style name of this compute command
<LI>cutoff = distance within which to label atoms as part of same cluster (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all cluster/atom 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that assigns each atom a cluster ID.
</P>
<P>A cluster is defined as a set of atoms, each of which is within the
cutoff distance from one or more other atoms in the cluster. If an
atom has no neighbors within the cutoff distance, then it is a 1-atom
cluster. The ID of every atom in the cluster will be the smallest
atom ID of any atom in the cluster.
</P>
<P>Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
<I>clsuter/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed 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>The per-atom vector values will be an ID > 0, as explained above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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doc/compute_cluster_atom.txt Normal file
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@ -0,0 +1,57 @@
"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 cluster/atom command :h3
[Syntax:]
compute ID group-ID cluster/atom cutoff :pre
ID, group-ID are documented in "compute"_compute.html command
cluster/atom = style name of this compute command
cutoff = distance within which to label atoms as part of same cluster (distance units) :ul
[Examples:]
compute 1 all cluster/atom 1.0 :pre
[Description:]
Define a computation that assigns each atom a cluster ID.
A cluster is defined as a set of atoms, each of which is within the
cutoff distance from one or more other atoms in the cluster. If an
atom has no neighbors within the cutoff distance, then it is a 1-atom
cluster. The ID of every atom in the cluster will be the smallest
atom ID of any atom in the cluster.
Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
{clsuter/atom} style.
[Output info:]
This compute calculates a per-atom vector, which can be accessed 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.
The per-atom vector values will be an ID > 0, as explained above.
[Restrictions:] none
[Related commands:]
"compute coord/atom"_compute_coord_atom.html
[Default:] none

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@ -54,7 +54,9 @@ above.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_cluster_atom.html">compute cluster/atom</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_coord_atom.txt
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@ -51,6 +51,8 @@ above.
[Restrictions:] none
[Related commands:] none
[Related commands:]
"compute cluster/atom"_compute_cluster_atom.html
[Default:] none