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11
doc/compute_ackland_atom.html
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@ -25,14 +25,14 @@
<P><B>Description:</B>
</P>
<P>Defines a computation that calculates the local lattice structure
according to <A HREF = "#Ackland">(Ackland)</A>.
according to the formulation given in <A HREF = "#Ackland">(Ackland)</A>.
</P>
<P>In contrast to the <A HREF = "compute_centro_atom.html">centro-symmetry
parameter</A> this method is stable against
temperature boost, because it is based not on the distance between
particles but the angles. Therefore statistical fluctuations are
averaged out a little more. A comparison with the Common Neighbor
Analysis metric is made in the paper..
Analysis metric is made in the paper.
</P>
<P>The result is a number which is mapped to the following different
lattice structures:
@ -49,6 +49,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.-
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

11
doc/compute_ackland_atom.txt
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@ -22,14 +22,14 @@ compute 1 all ackland/atom :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to "(Ackland)"_#Ackland.
according to the formulation given in "(Ackland)"_#Ackland.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
temperature boost, because it is based not on the distance between
particles but the angles. Therefore statistical fluctuations are
averaged out a little more. A comparison with the Common Neighbor
Analysis metric is made in the paper..
Analysis metric is made in the paper.
The result is a number which is mapped to the following different
lattice structures:
@ -46,6 +46,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.-
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed 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.
[Restrictions:] none
[Related commands:]

7
doc/compute_centro_atom.html
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@ -50,6 +50,13 @@ 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>centro/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none

7
doc/compute_centro_atom.txt
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@ -47,6 +47,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
{centro/atom} style.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed 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.
[Restrictions:] none
[Related commands:] none

7
doc/compute_coord_atom.html
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@ -42,6 +42,13 @@ 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>coord/atom</I> style.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none

7
doc/compute_coord_atom.txt
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@ -39,6 +39,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
{coord/atom} style.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed 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.
[Restrictions:] none
[Related commands:] none

61
doc/compute_displace_atom.html Normal file
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@ -0,0 +1,61 @@
<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 displace/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID displace/atom fix-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>displace/atom = style name of this compute command
<LI>fix-ID = ID of a fix of style <A HREF = "fix_coord_original.html">coord/original</A>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all displace/atom myCoords
</PRE>
<P><B>Description:</B>
</P>
<P>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. The original
coordinates are stored by a <A HREF = "fix_coord_original.html">fix
coord/original</A> command, whose ID must be
specified with this compute. They are the coordinates at the time the
fix command was issued. The displacement can be output directly via
the <A HREF = "dump.html">dump custom</A> command. It could also be used to
calculate a diffusion coefficient for a group of atoms, as is done by
the <A HREF = "fix_msd.html">fix msd</A> command.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group. Note that the fix defines its own group and
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
</P>
<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. The first 3 components of the vector are
the x,y,z displacements. The 4th component is the total displacement,
i.e. sqrt(dx*dx + dy*dy + dz*dz).
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>, <A HREF = "fix_msd.html">fix msd</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

56
doc/compute_displace_atom.txt Normal file
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@ -0,0 +1,56 @@
"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 displace/atom command :h3
[Syntax:]
compute ID group-ID displace/atom fix-ID :pre
ID, group-ID are documented in "compute"_compute.html command
displace/atom = style name of this compute command
fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul
[Examples:]
compute 1 all displace/atom myCoords :pre
[Description:]
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. The original
coordinates are stored by a "fix
coord/original"_fix_coord_original.html command, whose ID must be
specified with this compute. They are the coordinates at the time the
fix command was issued. The displacement can be output directly via
the "dump custom"_dump.html command. It could also be used to
calculate a diffusion coefficient for a group of atoms, as is done by
the "fix msd"_fix_msd.html command.
The value of the displacement will be 0.0 for atoms not in the
specified compute group. Note that the fix defines its own group and
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
[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. The first 3 components of the vector are
the x,y,z displacements. The 4th component is the total displacement,
i.e. sqrt(dx*dx + dy*dy + dz*dz).
[Restrictions:] none
[Related commands:]
"dump custom"_dump.html, "fix msd"_fix_msd.html
[Default:] none

7
doc/compute_ke_atom.html
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@ -33,6 +33,13 @@ specified compute group.
<P>The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

7
doc/compute_ke_atom.txt
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@ -30,6 +30,13 @@ specified compute group.
The kinetic energy is simply 1/2 m v^2, where m is the mass and v is
the velocity of each atom.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed 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.
[Restrictions:] none
[Related commands:]

7
doc/compute_pe_atom.html
View File

@ -55,6 +55,13 @@ E.g. 1/4 of the dihedral energy to each of the 4 atoms.
pairwise interactions between 1-4 atoms. The energy contribution of
these terms is included in the pair energy, not the dihedral energy.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

7
doc/compute_pe_atom.txt
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@ -52,6 +52,13 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates
pairwise interactions between 1-4 atoms. The energy contribution of
these terms is included in the pair energy, not the dihedral energy.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed 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.
[Restrictions:] none
[Related commands:]

15
doc/compute_stress_atom.html
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@ -33,9 +33,10 @@ tensor for each atom in a group. The tensor for each atom has 6
components: xx, yy, zz, xy, xz, yz. See the <A HREF = "compute_pressure.html">compute
pressure</A> command if you want the stress tensor
(pressure) of the entire system. The 6 components can be accessed by
indices 1-6 by any command that uses per-atom computes, e.g. the <A HREF = "dump.html">dump
custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
indices 1-6 by any command that uses per-atom computes as input,
e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview.
</P>
<P>The stress tensor for atom <I>I</I> is given by the following formula,
@ -97,6 +98,14 @@ possible to compute. There are also a few pair styles for manybody
potentials that are not yet instrumented to yield per-atom stress.
See the Restrictions below.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a vector of length 6 for each atom, which can
be accessed by indices 1-6 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. The 6 components of the vector are ordered
xx, yy, zz, xy, xz, yz.
</P>
<P><B>Restrictions:</B>
</P>
<P>These pair styles do not yet tabulate per-atom virial information to

15
doc/compute_stress_atom.txt
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@ -29,9 +29,10 @@ tensor for each atom in a group. The tensor for each atom has 6
components: xx, yy, zz, xy, xz, yz. See the "compute
pressure"_compute_pressure.html command if you want the stress tensor
(pressure) of the entire system. The 6 components can be accessed by
indices 1-6 by any command that uses per-atom computes, e.g. the "dump
custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
command or "fix ave/atom"_fix_ave_atom.html command. See "this
indices 1-6 by any command that uses per-atom computes as input,
e.g. the "dump custom"_dump.html command or "fix
ave/spatial"_fix_ave_spatial.html command or "fix
ave/atom"_fix_ave_atom.html command. See "this
section"_Section_howto.html#4_15 for an overview.
The stress tensor for atom {I} is given by the following formula,
@ -93,6 +94,14 @@ possible to compute. There are also a few pair styles for manybody
potentials that are not yet instrumented to yield per-atom stress.
See the Restrictions below.
[Output info:]
This compute calculates a vector of length 6 for each atom, which can
be accessed by indices 1-6 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. The 6 components of the vector are ordered
xx, yy, zz, xy, xz, yz.
[Restrictions:]
These pair styles do not yet tabulate per-atom virial information to

2
doc/fix_ave_atom.html
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@ -53,7 +53,7 @@ ave/spatial</A> or <A HREF = "dump.html">dump custom</A> commands.
</P>
<P>Each listed value is averaged independently. The group specified with
the command means only atoms within the group have their averages
computed. Atoms not in the group have their result set to 0.0.
computed. Atoms not in the group have their result(s) set to 0.0.
</P>
<P>Each listed value can be an atom attribute (position, velocity, force
component) or can be the result of a <A HREF = "compute.html">compute</A> or

2
doc/fix_ave_atom.txt
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@ -42,7 +42,7 @@ ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands.
Each listed value is averaged independently. The group specified with
the command means only atoms within the group have their averages
computed. Atoms not in the group have their result set to 0.0.
computed. Atoms not in the group have their result(s) set to 0.0.
Each listed value can be an atom attribute (position, velocity, force
component) or can be the result of a "compute"_compute.html or