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10
doc/Section_commands.html
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@ -347,11 +347,11 @@ 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_bond_local.html">bond/local</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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><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></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><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><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></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_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><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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_gyration.html">gyration</A></TD><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></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
<TR ALIGN="center"><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><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

2
doc/Section_commands.txt
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@ -465,6 +465,7 @@ each style or click on the style itself for a full description:
"com"_compute_com.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/sphere"_compute_erotate_sphere.html,
@ -472,6 +473,7 @@ each style or click on the style itself for a full description:
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"msd"_compute_msd.html,

2
doc/compute.html
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@ -173,6 +173,7 @@ available in LAMMPS:
<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_dihedral_local.html">dihedral/local</A> - angle of each dihedral
<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
@ -180,6 +181,7 @@ available in LAMMPS:
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms

2
doc/compute.txt
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@ -168,6 +168,7 @@ available in LAMMPS:
"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
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
"displace/atom"_compute_displace_atom.html - displacement of each atom
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
@ -175,6 +176,7 @@ available in LAMMPS:
"group/group"_compute_group_group.html - energy/force between two groups of atoms
"gyration"_compute_gyration.html - radius of gyration of group of atoms
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"improper/local"_compute_improper_local.html - angle of each improper
"ke"_compute_ke.html - translational kinetic energy
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"msd"_compute_msd.html - mean-squared displacement of group of atoms

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@ -21,17 +21,17 @@
<LI>zero or more keywords may be appended
<LI>keyword = <I>theta</I> or <I>energy</I>
<LI>keyword = <I>theta</I> or <I>eng</I>
<PRE> <I>theta</I> = tabulate angles
<I>energy</I> = tabulate angle energies
<I>eng</I> = tabulate angle energies
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all angle/local theta
compute 1 all angle/local theta energy
compute 1 all angle/local eng theta
</PRE>
<P><B>Description:</B>
</P>
@ -40,10 +40,16 @@ The number of datums generated, aggregated across all processors,
equals the number of angles in the system.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only be
included if all 3 atoms in the angle are in the specified compute group.
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
group. Any angles that have been broken (see the
<A HREF = "angle_style.html">angle_style</A> command) by setting their angle type to
0 are not included. Angles that have been turned off (see the <A HREF = "fix_shake.html">fix
shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> commands) by
setting their angle type negative are written into the file, but their
energy will be 0.0.
</P>
<P>The output <I>theta</I> will be in degrees. The output <I>energy</I> will be in
<P>The output <I>theta</I> will be in degrees. The output <I>eng</I> will be in
energy <A HREF = "units.html">units</A>.
</P>
<P>Note that as atoms migrate from processor to processor, there will be

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doc/compute_angle_local.txt
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@ -15,15 +15,15 @@ compute ID group-ID angle/local input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
angle/local = style name of this compute command :l
zero or more keywords may be appended :l
keyword = {theta} or {energy} :l
keyword = {theta} or {eng} :l
{theta} = tabulate angles
{energy} = tabulate angle energies :pre
{eng} = tabulate angle energies :pre
:ule
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local theta energy :pre
compute 1 all angle/local eng theta :pre
[Description:]
@ -32,10 +32,16 @@ The number of datums generated, aggregated across all processors,
equals the number of angles in the system.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only be
included if all 3 atoms in the angle are in the specified compute group.
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
group. Any angles that have been broken (see the
"angle_style"_angle_style.html command) by setting their angle type to
0 are not included. Angles that have been turned off (see the "fix
shake"_fix_shake.html or "delete_bonds"_delete_bonds.html commands) by
setting their angle type negative are written into the file, but their
energy will be 0.0.
The output {theta} will be in degrees. The output {energy} will be in
The output {theta} will be in degrees. The output {eng} will be in
energy "units"_units.html.
Note that as atoms migrate from processor to processor, there will be

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doc/compute_bond_local.html
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@ -21,17 +21,17 @@
<LI>zero or more keywords may be appended
<LI>keyword = <I>distance</I> or <I>energy</I>
<LI>keyword = <I>dist</I> or <I>eng</I>
<PRE> <I>distance</I> = tabulate bond distances
<I>energy</I> = tablutate bond energies
<PRE> <I>dist</I> = tabulate bond distances
<I>eng</I> = tablutate bond energies
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all bond/local energy
compute 1 all bond/local distance energy
<PRE>compute 1 all bond/local eng
compute 1 all bond/local dist eng
</PRE>
<P><B>Description:</B>
</P>
@ -42,9 +42,14 @@ equals the number of bonds in the system.
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
Any bonds that have been broken (see the <A HREF = "bond_style.html">bond_style</A>
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the <A HREF = "fix_shake.html">fix shake</A> or
<A HREF = "delete_bonds.html">delete_bonds</A> commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.
</P>
<P>The output <I>distance</I> will be in distance <A HREF = "units.html">units</A>. The
output <I>energy</I> will be in energy <A HREF = "units.html">units</A>.
<P>The output <I>dist</I> will be in distance <A HREF = "units.html">units</A>. The output
<I>eng</I> will be in energy <A HREF = "units.html">units</A>.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array

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doc/compute_bond_local.txt
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@ -15,15 +15,15 @@ compute ID group-ID bond/local input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
bond/local = style name of this compute command :l
zero or more keywords may be appended :l
keyword = {distance} or {energy} :l
{distance} = tabulate bond distances
{energy} = tablutate bond energies :pre
keyword = {dist} or {eng} :l
{dist} = tabulate bond distances
{eng} = tablutate bond energies :pre
:ule
[Examples:]
compute 1 all bond/local energy
compute 1 all bond/local distance energy :pre
compute 1 all bond/local eng
compute 1 all bond/local dist eng :pre
[Description:]
@ -34,9 +34,14 @@ equals the number of bonds in the system.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
Any bonds that have been broken (see the "bond_style"_bond_style.html
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the "fix shake"_fix_shake.html or
"delete_bonds"_delete_bonds.html commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.
The output {distance} will be in distance "units"_units.html. The
output {energy} will be in energy "units"_units.html.
The output {dist} will be in distance "units"_units.html. The output
{eng} will be in energy "units"_units.html.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array

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@ -0,0 +1,78 @@
<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 dihedral/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID dihedral/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>dihedral/local = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>phi</I>
<PRE> <I>phi</I> = tabulate dihedral angles
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all dihedral/local phi
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual
dihedrals. The number of datums generated, aggregated across all
processors, equals the number of angles in the system.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
compute group.
</P>
<P>The output <I>phi</I> will be in degrees.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, dihedral output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local 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>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,68 @@
"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 dihedral/local command :h3
[Syntax:]
compute ID group-ID dihedral/local input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
dihedral/local = style name of this compute command :l
zero or more keywords may be appended :l
keyword = {phi} :l
{phi} = tabulate dihedral angles :pre
:ule
[Examples:]
compute 1 all dihedral/local phi :pre
[Description:]
Define a computation that calculates properties of individual
dihedrals. The number of datums generated, aggregated across all
processors, equals the number of angles in the system.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
compute group.
The output {phi} will be in degrees.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, dihedral output from the "compute
property/local"_compute_property_local.html command can be combined
with data from this command and output by the "dump local"_dump.html
command in a consistent way.
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
[Restrictions:] none
[Related commands:]
"dump local"_dump.html, "compute
property/local"_compute_property_local.html
[Default:] none

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@ -0,0 +1,78 @@
<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 improper/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID improper/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>improper/local = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>chi</I>
<PRE> <I>chi</I> = tabulate improper angles
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all improper/local chi
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual improper
interactions. The number of datums generated, aggregated across all
processors, equals the number of impropers in the system.
</P>
<P>The local data stored by this command is generated by looping over all
the atoms owned on a processor and their impropers. An improper will
only be included if all 4 atoms in the improper are in the specified
compute group.
</P>
<P>The output <I>chi</I> will be in degrees.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, improper output from the <A HREF = "compute_property_local.html">compute
property/local</A> command can be combined
with data from this command and output by the <A HREF = "dump.html">dump local</A>
command in a consistent way.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local 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>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump local</A>, <A HREF = "compute_property_local.html">compute
property/local</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,68 @@
"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 improper/local command :h3
[Syntax:]
compute ID group-ID improper/local input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
improper/local = style name of this compute command :l
zero or more keywords may be appended :l
keyword = {chi} :l
{chi} = tabulate improper angles :pre
:ule
[Examples:]
compute 1 all improper/local chi :pre
[Description:]
Define a computation that calculates properties of individual improper
interactions. The number of datums generated, aggregated across all
processors, equals the number of impropers in the system.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their impropers. An improper will
only be included if all 4 atoms in the improper are in the specified
compute group.
The output {chi} will be in degrees.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, improper output from the "compute
property/local"_compute_property_local.html command can be combined
with data from this command and output by the "dump local"_dump.html
command in a consistent way.
[Output info:]
This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the
array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
[Restrictions:] none
[Related commands:]
"dump local"_dump.html, "compute
property/local"_compute_property_local.html
[Default:] none