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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2076 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2008-08-20 14:56:12 +00:00
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26
doc/neighbor.html
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@ -33,13 +33,6 @@ need to be built, but more pairs must be checked for possible force
interactions every timestep. The default value for <I>skin</I> depends on
the choice of units for the simulation (see below).
</P>
<P>For simulations without pairwise interactions (see "pair_style none"
command), and just bonded interactions, you still need to set the
neighbor skin distance. Pairwise neighbor lists will not be formed
but the skin distance also determines which atoms are communicated
from nearby processors, so it should be slightly large enough that all
bond, angle, etc atoms are acquired.
</P>
<P>The <I>style</I> value selects what algorithm is used to build the list.
The <I>bin</I> style creates the list by binning which is an operation that
scales linearly with N/P, the number of atoms per processor where N =
@ -71,7 +64,24 @@ the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See <A HREF = "Section_start.html#2_7">this
section</A> for details.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>For simulations without pairwise interactions (see "pair_style none"
command), but that include bonded interactions, you still need to set
the neighbor skin distance. Pairwise neighbor lists will not be
formed, but the pair cutoff (0.0 in this case) plus the skin distance
is the range at which atoms are communicated from nearby processors.
This needs to be large enough that atoms in the same bond, angle, etc
as an atom owned by a processor are acquired. What distance is
appropriate depends on the <A HREF = "newton.html">newton bond</A> setting. For
newton bond off, the distance needs to be the furthest distance
between any two atoms in the bond, angle, etc. E.g. the distance
between the 1-4 atoms in a dihedral. For newton bond on, the distance
is between the central atom in the bond, angle, etc and any other
atom. E.g. the distance between the 2-4 atoms in a dihedral.
</P>
<P>The same logic applies to systems that include bonded interactions and
a pairwise cutoff shorter than the distances just described.
</P>
<P><B>Related commands:</B>
</P>

26
doc/neighbor.txt
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@ -30,13 +30,6 @@ need to be built, but more pairs must be checked for possible force
interactions every timestep. The default value for {skin} depends on
the choice of units for the simulation (see below).
For simulations without pairwise interactions (see "pair_style none"
command), and just bonded interactions, you still need to set the
neighbor skin distance. Pairwise neighbor lists will not be formed
but the skin distance also determines which atoms are communicated
from nearby processors, so it should be slightly large enough that all
bond, angle, etc atoms are acquired.
The {style} value selects what algorithm is used to build the list.
The {bin} style creates the list by binning which is an operation that
scales linearly with N/P, the number of atoms per processor where N =
@ -68,7 +61,24 @@ the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See "this
section"_Section_start.html#2_7 for details.
[Restrictions:] none
[Restrictions:]
For simulations without pairwise interactions (see "pair_style none"
command), but that include bonded interactions, you still need to set
the neighbor skin distance. Pairwise neighbor lists will not be
formed, but the pair cutoff (0.0 in this case) plus the skin distance
is the range at which atoms are communicated from nearby processors.
This needs to be large enough that atoms in the same bond, angle, etc
as an atom owned by a processor are acquired. What distance is
appropriate depends on the "newton bond"_newton.html setting. For
newton bond off, the distance needs to be the furthest distance
between any two atoms in the bond, angle, etc. E.g. the distance
between the 1-4 atoms in a dihedral. For newton bond on, the distance
is between the central atom in the bond, angle, etc and any other
atom. E.g. the distance between the 2-4 atoms in a dihedral.
The same logic applies to systems that include bonded interactions and
a pairwise cutoff shorter than the distances just described.
[Related commands:]

28
doc/set.html
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@ -13,7 +13,7 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>set style ID keyword value ...
<PRE>set style ID keyword values ...
</PRE>
<UL><LI>style = <I>atom</I> or <I>group</I> or <I>region</I>
@ -21,7 +21,7 @@
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>diameter</I> or <I>density</I> or <I>volume</I> or
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>diameter</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
<I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<PRE> <I>type</I> value = atom type
@ -45,6 +45,8 @@
<I>diameter</I> value = particle diameter (distance units)
<I>density</I> value = particle density (mass/distance^3 units)
<I>volume</I> value = particle volume (distance^3 units)
<I>image</I> nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
<I>bond</I> value = bond type for all bonds between selected atoms
<I>angle</I> value = angle type for all angles between selected atoms
<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
@ -150,6 +152,28 @@ combined with its density determines their mass.
</P>
<P>Keyword <I>volume</I> sets the effective size of all selected particles.
</P>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An
image of 0 means it is inside the box as defined. A value of 2 means
add 2 box lengths to get the true value. A value of -1 means subtract
1 box length to get the true value. LAMMPS updates these flags as
atoms cross periodic boundaries during the simulation. The flags can
be output with atom snapshots via the <A HREF = "dump.html">dump</A> command. If a
value of NULL is specified for any of nx,ny,nz, then the current image
value for that dimension is unchanged.
</P>
<P>This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the <A HREF = "fix_msd.html">fix msd</A>
command. Care should be taken not to reset the image flags of two
atoms in a bond to the same value if the bond straddles a periodic
boundary (rather they should be different by +/- 1). This will not
affect the dynamics of a simulation, but may mess up analysis of the
trajectories if a LAMMPS diagnostic or your own analysis relies on the
image flags to unwrap a molecule which straddles the periodic box.
</P>
<P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
style</A> being used must support the use of those
parameters. For example, granular particles store a diameter and

28
doc/set.txt
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@ -10,7 +10,7 @@ set command :h3
[Syntax:]
set style ID keyword value ... :pre
set style ID keyword values ... :pre
style = {atom} or {group} or {region} :ulb,l
ID = atom ID or group ID or region ID :l
@ -18,7 +18,7 @@ one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or \
{x} or {y} or {z} or {vx} or {vy} or {vz} or \
{charge} or {dipole} or {dipole/random} or {quat/random} or \
{diameter} or {density} or {volume} or
{diameter} or {density} or {volume} or {image} or
{bond} or {angle} or {dihedral} or {improper} :l
{type} value = atom type
{type/fraction} values = type fraction seed
@ -41,6 +41,8 @@ keyword = {type} or {type/fraction} or {mol} or \
{diameter} value = particle diameter (distance units)
{density} value = particle density (mass/distance^3 units)
{volume} value = particle volume (distance^3 units)
{image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
{bond} value = bond type for all bonds between selected atoms
{angle} value = angle type for all angles between selected atoms
{dihedral} value = dihedral type for all dihedrals between selected atoms
@ -145,6 +147,28 @@ combined with its density determines their mass.
Keyword {volume} sets the effective size of all selected particles.
Keyword {image} sets which image of the simulation box the atom is
considered to be in. It is only applied to periodic dimensions. An
image of 0 means it is inside the box as defined. A value of 2 means
add 2 box lengths to get the true value. A value of -1 means subtract
1 box length to get the true value. LAMMPS updates these flags as
atoms cross periodic boundaries during the simulation. The flags can
be output with atom snapshots via the "dump"_dump.html command. If a
value of NULL is specified for any of nx,ny,nz, then the current image
value for that dimension is unchanged.
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the "fix msd"_fix_msd.html
command. Care should be taken not to reset the image flags of two
atoms in a bond to the same value if the bond straddles a periodic
boundary (rather they should be different by +/- 1). This will not
affect the dynamics of a simulation, but may mess up analysis of the
trajectories if a LAMMPS diagnostic or your own analysis relies on the
image flags to unwrap a molecule which straddles the periodic box.
For the {diameter} and {density} and {volume} keywords, the "atom
style"_atom_style.html being used must support the use of those
parameters. For example, granular particles store a diameter and