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2009-12-22 00:22:16 +00:00
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16
doc/Section_commands.html
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@ -321,14 +321,14 @@ of 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 = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_store_coord.html">store/coord</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -389,7 +389,6 @@ of each style or click on the style itself for a full description:
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"coord/original"_fix_coord_original.html,
"deform"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
@ -432,6 +431,8 @@ of each style or click on the style itself for a full description:
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"store/coord"_fix_store_coord.html,
"store/force"_fix_store_force.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,

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doc/compute_displace_atom.html
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@ -35,20 +35,20 @@ dz*dz).
</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,
the compute creates its own fix of style "coord/original", as if this
the compute creates its own fix of style "store/coord", as if this
command had been issued:
</P>
<PRE>fix compute-ID_coord_original group-ID coord/original
<PRE>fix compute-ID_store_coord group-ID store/coord
</PRE>
<P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
the same as the compute group.
<P>See the <A HREF = "fix_coord_original.html">fix store/coord</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
</P>
<P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store/coord 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
@ -83,8 +83,8 @@ overview of LAMMPS output options.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_coord_original.html">fix
coord/original</A>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_coord.html">fix
store/coord</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_displace_atom.txt
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@ -32,20 +32,20 @@ dz*dz).
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
the compute creates its own fix of style "store/coord", as if this
command had been issued:
fix compute-ID_coord_original group-ID coord/original :pre
fix compute-ID_store_coord group-ID store/coord :pre
See the "fix coord/original"_fix_coord_original.html command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
the same as the compute group.
See the "fix store/coord"_fix_coord_original.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.
The value of the displacement will be 0.0 for atoms not in the
specified compute group.
IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
IMPORTANT NOTE: Fix store/coord 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
@ -81,6 +81,6 @@ overview of LAMMPS output options.
[Related commands:]
"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
coord/original"_fix_coord_original.html
store/coord"_fix_store_coord.html
[Default:] none

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@ -49,22 +49,22 @@ 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,
the compute creates its own fix of style "coord/original", as if this
the compute creates its own fix of style "store/coord", as if this
command had been issued:
</P>
<PRE>fix compute-ID_coord_original group-ID coord/original
<PRE>fix compute-ID_store_coord group-ID store/coord
</PRE>
<P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for
<P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
underscore + "store_coord", and the group for the new fix is
the same as the compute group.
</P>
<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 displacment of each atom is calcluated. The <I>com</I> option
is also passed to the created fix coord/original.
is also passed to the created fix store/coord.
</P>
<P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store/coord 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
@ -102,8 +102,8 @@ number of atoms in the simulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_coord_original.html">fix
coord/original</A>, <A HREF = "compute_msd_molecule.html">compute
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store_coord.html">fix
store/coord</A>, <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A>
</P>
<P><B>Default:</B>

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doc/compute_msd.txt
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@ -41,22 +41,22 @@ 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,
the compute creates its own fix of style "coord/original", as if this
the compute creates its own fix of style "store/coord", as if this
command had been issued:
fix compute-ID_coord_original group-ID coord/original :pre
fix compute-ID_store_coord group-ID store/coord :pre
See the "fix coord/original"_fix_coord_original.html command for
See the "fix store/coord"_fix_store_coord.html command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
underscore + "store_coord", 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 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 passed to the created fix coord/original.
is also passed to the created fix store/coord.
IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
IMPORTANT NOTE: Fix store/coord 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
@ -95,7 +95,7 @@ number of atoms in the simulation.
[Related commands:]
"compute displace_atom"_compute_displace_atom.html, "fix
coord/original"_fix_coord_original.html, "compute
store/coord"_fix_store_coord.html, "compute
msd/molecule"_compute_msd_molecule.html
[Default:]

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@ -9,54 +9,55 @@
<HR>
<H3>compute bond/local command
<H3>compute pair/local command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID bond/local input1 input2 ...
<PRE>compute ID group-ID pair/local input1 input2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>bond/local = style name of this compute command
<LI>pair/local = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>dist</I> or <I>eng</I>
<LI>keyword = <I>dist</I> or <I>eng</I> or <I>force</I>
<PRE> <I>dist</I> = tabulate bond distances
<I>eng</I> = tablutate bond energies
<PRE> <I>dist</I> = tabulate pairwise distances
<I>eng</I> = tablutate pairwise energies
<I>eng</I> = tablutate pairwise forces
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all bond/local eng
compute 1 all bond/local dist eng
<PRE>compute 1 all pair/local eng
compute 1 all pair/local dist eng force
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates properties of individual bond
<P>Define a computation that calculates properties of individual pairwise
interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system.
processors, equals the number of pairwise interactions 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 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>The local data stored by this command is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
commands.
</P>
<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>.
<I>eng</I> will be in energy <A HREF = "units.html">units</A>. The output <I>force</I> will
be in force <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
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, bond output from the <A HREF = "compute_property_local.html">compute
For example, pair 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.
@ -65,7 +66,7 @@ command in a consistent way.
</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 bonds. If a single keyword is specified, a
array is the number of pairs. 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

43
doc/compute_pair_local.txt
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@ -6,49 +6,50 @@
:line
compute bond/local command :h3
compute pair/local command :h3
[Syntax:]
compute ID group-ID bond/local input1 input2 ... :pre
compute ID group-ID pair/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
pair/local = style name of this compute command :l
zero or more keywords may be appended :l
keyword = {dist} or {eng} :l
{dist} = tabulate bond distances
{eng} = tablutate bond energies :pre
keyword = {dist} or {eng} or {force} :l
{dist} = tabulate pairwise distances
{eng} = tablutate pairwise energies
{eng} = tablutate pairwise forces :pre
:ule
[Examples:]
compute 1 all bond/local eng
compute 1 all bond/local dist eng :pre
compute 1 all pair/local eng
compute 1 all pair/local dist eng force :pre
[Description:]
Define a computation that calculates properties of individual bond
Define a computation that calculates properties of individual pairwise
interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system.
processors, equals the number of pairwise interactions 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 local data stored by this command is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
commands.
The output {dist} will be in distance "units"_units.html. The output
{eng} will be in energy "units"_units.html.
{eng} will be in energy "units"_units.html. The output {force} will
be in force "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
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, bond output from the "compute
For example, pair 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.
@ -57,7 +58,7 @@ command in a consistent way.
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 bonds. If a single keyword is specified, a
array is the number of pairs. 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

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@ -60,21 +60,22 @@ attributes can be specified together, or angle attributes, etc. Bond
and angle attributes can not be mixed in the same compute
property/local command.
</P>
<P>The local data is generated by looping over all the atoms owned on a
processor and extracting bond, angle, etc info. For bonds, info about
an individual bond will only be included if both atoms in the bond are
in the specified compute group. Likewise for angles, dihedrals, etc.
<P>If the inputs are pair attributes, the local data is generated by
looping over the pairwise neighbor list. Info about an individual
pairwise interaction will only be included if both atoms in the pair
are in the specified compute group, and if the current pairwise
distance is less than the force cutoff distance for that interaction,
as defined by the <A HREF = "pair_style.html">pair_style</A> and
<A HREF = "pair_coeff.html">pair_coeff</A> commands.
</P>
<P>In the case of pairs, the local data is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
commands.
<P>If the inputs are bond, angle, etc attributes, the local data is
generated by looping over all the atoms owned on a processor and
extracting bond, angle, etc info. For bonds, info about an individual
bond will only be included if both atoms in the bond are in the
specified compute group. Likewise for angles, dihedrals, etc.
</P>
<P>As atoms migrate from processor to processor, there will be no
consistent ordering of the entries within the local vector or array
<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.

27
doc/compute_property_local.txt
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@ -53,21 +53,22 @@ attributes can be specified together, or angle attributes, etc. Bond
and angle attributes can not be mixed in the same compute
property/local command.
The local data is generated by looping over all the atoms owned on a
processor and extracting bond, angle, etc info. For bonds, info about
an individual bond will only be included if both atoms in the bond are
in the specified compute group. Likewise for angles, dihedrals, etc.
If the inputs are pair attributes, the local data is generated by
looping over the pairwise neighbor list. Info about an individual
pairwise interaction will only be included if both atoms in the pair
are in the specified compute group, and if the current pairwise
distance is less than the force cutoff distance for that interaction,
as defined by the "pair_style"_pair_style.html and
"pair_coeff"_pair_coeff.html commands.
In the case of pairs, the local data is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
commands.
If the inputs are bond, angle, etc attributes, the local data is
generated by looping over all the atoms owned on a processor and
extracting bond, angle, etc info. For bonds, info about an individual
bond will only be included if both atoms in the bond are in the
specified compute group. Likewise for angles, dihedrals, etc.
As atoms migrate from processor to processor, there will be no
consistent ordering of the entries within the local vector or array
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.

3
doc/fix.html
View File

@ -168,7 +168,6 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_bond_create.html">bond/create</A> - create bonds on the fly
<LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping
<LI><A HREF = "fix_box_relax.html">box/relax</A> - relax box size during energy minimization
<LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom
<LI><A HREF = "fix_deform.html">deform</A> - change the simulation box size/shape
<LI><A HREF = "fix_deposit.html">deposit</A> - add new atoms above a surface
<LI><A HREF = "fix_drag.html">drag</A> - drag atoms towards a defined coordinate
@ -210,6 +209,8 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_spring.html">spring</A> - apply harmonic spring force to group of atoms
<LI><A HREF = "fix_spring_rg.html">spring/rg</A> - spring on radius of gyration of group of atoms
<LI><A HREF = "fix_spring_self.html">spring/self</A> - spring from each atom to its origin
<LI><A HREF = "fix_store_coord.html">store/coord</A> - store coords of each atom
<LI><A HREF = "fix_store_force.html">store/force</A> - store force on each atom
<LI><A HREF = "fix_temp_berendsen.html">temp/berendsen</A> - temperature control by Berendsen thermostat
<LI><A HREF = "fix_temp_rescale.html">temp/rescale</A> - temperature control by velocity rescaling
<LI><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A> - Muller-Plathe kinetic energy exchange for thermal conductivity calculation

3
doc/fix.txt
View File

@ -163,7 +163,6 @@ list of fix styles available in LAMMPS:
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"coord/original"_fix_coord_original.html - store original coords of each atom
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"drag"_fix_drag.html - drag atoms towards a defined coordinate
@ -211,6 +210,8 @@ list of fix styles available in LAMMPS:
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
group of atoms
"spring/self"_fix_spring_self.html - spring from each atom to its origin
"store/coord"_fix_store_coord.html - store coords of each atom
"store/force"_fix_store_force.html - store force on each atom
"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
Berendsen thermostat
"temp/rescale"_fix_temp_rescale.html - temperature control by \

0
doc/fix_coord_original.html → doc/fix_store_coord.html
View File

0
doc/fix_coord_original.txt → doc/fix_store_coord.txt
View File