Commit d7a06944 authored by sjplimp's avatar sjplimp
Browse files

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3565 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent d6202909
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@@ -19,7 +19,7 @@

<LI>group-ID = ID of the group of atoms to be dumped 

<LI>style = <I>atom</I> or <I>bond</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>custom</I> 
<LI>style = <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> 

<LI>N = dump every this many timesteps 

@@ -28,12 +28,20 @@
<LI>args = list of arguments for a particular style 

<PRE>  <I>atom</I> args = none
  <I>bond</I> args = none
  <I>cfg</I> args = same as <I>custom</I> args, see below
  <I>dcd</I> args = none
  <I>xtc</I> args = none
  <I>xyz</I> args = none 
  <I>custom</I> args = list of atom attributes
</PRE>
<PRE>  <I>local</I> args = list of local attributes
    possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
      index = enumeration of local values
      c_ID = local vector calculated by a compute with ID
      c_ID[N] = Nth column of local array calculated by a compute with ID
      f_ID = local vector calculated by a fix with ID
      f_ID[N] = Nth column of local array calculated by a fix with ID 
</PRE>
<PRE>  <I>custom</I> args = list of atom attributes
    possible attributes = id, mol, type, mass,
			  x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
			  vx, vy, vz, fx, fy, fz,
@@ -60,9 +68,9 @@
      angmomx,angmomy,angmomz = angular momentum of extended particle
      quatw,quati,quatj,quatk = quaternion components for aspherical particles
      tqx,tqy,tqz = torque on extended particles
      c_ID = per-atom vector value calculated by a compute with ID
      c_ID = per-atom vector calculated by a compute with ID
      c_ID[N] = Nth column of per-atom array calculated by a compute with ID
      f_ID = per-atom vector value calculated by a fix with ID
      f_ID = per-atom vector calculated by a fix with ID
      f_ID[N] = Nth column of per-atom array calculated by a fix with ID
      v_name = per-atom vector calculated by an atom-style variable with name 
</PRE>
@@ -98,7 +106,7 @@ box.
dump files (typically one line per atom) may be written in an
indeterminate order.  This is because data for a single snapshot is
collected from multiple processors.  This is always the case for the
<I>atom</I>, <I>bond</I>, and <I>custom</I> styles.  It is also the case for the
<I>atom</I>, <I>local</I>, and <I>custom</I> styles.  It is also the case for the
<I>xyz</I> style if the dump group is not <I>all</I>.  It is not the case for
the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted order.
So does the <I>xyz</I> style if the dump group is <I>all</I>.  The <I>cfg</I> style
@@ -112,7 +120,7 @@ file and in what format. Settings made via the
<A HREF = "dump_modify.html">dump_modify</A> command can also alter the format of
individual values and the file itself.
</P>
<P>The <I>atom</I>, <I>bond</I>, and <I>custom</I> styles create files in a simple text
<P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
format that is self-explanatory when viewing a dump file.  Many of the
LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
@@ -139,16 +147,6 @@ boundaries. The format can be changed to unscaled coords via the
<A HREF = "dump_modify.html">dump_modify</A> settings.  Image flags can also be
added for each atom via dump_modify.
</P>
<P>For style <I>bond</I>, the bond topology between atoms is written, in the
same format specified in data files read in by the
<A HREF = "read_data.html">read_data</A> command.  Both atoms in the bond must be in
the dump group for the bond to be written.  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 written.  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.
</P>
<P>Style <I>custom</I> allows you to specify a list of atom attributes to be
written to the dump file for each atom.  Possible attributes are
listed above and will appear in the order specified.  You cannot
@@ -156,8 +154,20 @@ specify a quantity that is not defined for a particular simulation -
such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
assign charges.  Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep.  An explanation of the dump custom quantities is given
below.
the timestep.  An explanation of the possible dump custom attributes
is given below.
</P>
<P>For style <I>local</I>, local output generated by <A HREF = "compute.html">computes</A>
and <A HREF = "fix.html">fixes</A> is used to gnerate lines of output that is
written to the dump file.  This local data is typically calculated by
each processor based on the atoms it owns, but there may be zero or
more entities per atom, e.g. a list of bond distances.  An explanation
of the possible dump local attributes is given below.  Note that by
using input from the <A HREF = "compute_property_local.html">compute
property/local</A> command with dump local,
it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
extended CFG format files, as used by the
@@ -264,11 +274,54 @@ styles.
</P>
<HR>

<P>This section explains the atom quantities that can be specified as
<P>This section explains the local attributes that can be specified as
part of the <I>local</I> style.
</P>
<P>The <I>index</I> attribute can be used to generate an index number from 1
to N for each line written into the dump file, where N is the total
number of local datums from all processors, or lines of output that
will appear in the snapshot.  Note that because data from different
processors depend on what atoms they currently own, and atoms migrate
between processor, there is no guarantee that the same index will be
used for the same info (e.g. a particular bond) in successive
snapshots.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow local vectors or arrays
calculated by a <A HREF = "compute.html">compute</A> to be output.  The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script.  See the
<A HREF = "compute.html">compute</A> command for details.  There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
</P>
<P>Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command, and per-atom quantities can be
output by the dump custom command.
</P>
<P>If <I>c_ID</I> is used as a attribute, then the local vector calculated by
the compute is printed.  If <I>c_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow local vectors or arrays
calculated by a <A HREF = "fix.html">fix</A> to be output.  The ID in the attribute
should be replaced by the actual ID of the fix that has been defined
previously in the input script.
</P>
<P>If <I>f_ID</I> is used as a attribute, then the local vector calculated by
the fix is printed.  If <I>f_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the fix.
</P>
<HR>

<P>This section explains the atom attributes that can be specified as
part of the <I>custom</I> and <I>cfg</I> styles.
</P>
<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, <I>q</I> keywords are self-explanatory.
<I>fz</I>, <I>q</I> attributes are self-explanatory.
</P>
<P><I>Id</I> is the atom ID.  <I>Mol</I> is the molecule ID, included in the data
file for molecular systems.  <I>Type</I> is the atom type.  <I>Mass</I> is the
@@ -276,7 +329,7 @@ atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, an
of atom velocity and force and atomic charge.
</P>
<P>There are several options for outputting atom coordinates.  The <I>x</I>,
<I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc).  Use
<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0.  If the simluation box is triclinic
@@ -288,57 +341,58 @@ the coordinate would be if it had not been wrapped back into the
periodic box.  Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
coordinate values may be far outside the box bounds printed with the
snapshot.  The image flags can be printed directly using the <I>ix</I>,
<I>iy</I>, <I>iz</I> keywords. The <A HREF = "dump_modify.html">dump_modify</A> command
<I>iy</I>, <I>iz</I> attributes. The <A HREF = "dump_modify.html">dump_modify</A> command
describes in more detail what is meant by scaled vs unscaled
coordinates and the image flags.
</P>
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> keywords are specific to dipolar systems
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
defined with an atom style of <I>dipole</I>.  They give the orientation of
the atom's point dipole moment.
</P>
<P>The <I>radius</I> keyword is specific to extended spherical particles
<P>The <I>radius</I> attribute is specific to extended spherical particles
that have a finite size, such as granular particles defined with
an atom style of <I>granular</I>.
</P>
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> keywords are specific to extended
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to extended
spherical or aspherical particles that have an angular velocity.  Only
certain atom styles, such as <I>granular</I> or <I>dipole</I> define this
quantity.
</P>
<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> keywords are specific to
<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
extended aspherical particles that have an angular momentum.  Only
the <I>ellipsoid</I> atom style defines this quantity.
</P>
<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> keywords are for aspherical
<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> attributes are for aspherical
particles defined with an atom style of <I>ellipsoid</I>.  They are the
components of the quaternion that defines the orientation of the
particle.
</P>
<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> keywords are for extended spherical or
<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for extended spherical or
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector per-atom
quantities calculated by a <A HREF = "compute.html">compute</A> to be output.  The
ID in the keyword should be replaced by the actual ID of the compute
that has been defined previously in the input script.  See the
<A HREF = "compute.html">compute</A> command for details.  There are per-atom
computes for calculating the energy, stress, centro-symmetry
parameter, and coordination number of individual atoms.
</P>
<P>Note that computes which calculate global scalar and vector
quantities, as opposed to per-atom quantities, cannot be output in a
dump.  Instead, these quantities can be output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the compute is printed.  If <I>c_ID[N]</I> is used, then N
must be in the range from 1-M, which will print the Nth column of
the M-length per-atom array calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
calculated by a <A HREF = "compute.html">compute</A> to be output.  The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script.  See the
<A HREF = "compute.html">compute</A> command for details.  There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.
</P>
<P>Note that computes which calculate global or local quantities, as
opposed to per-atom quantities, cannot be output in a dump custom
command.  Instead, global quantities can be output by the
<A HREF = "thermo_style.html">thermo_style custom</A> command, and local quantities
can be output by the dump local command.
</P>
<P>If <I>c_ID</I> is used as a attribute, then the per-atom vector calculated
by the compute is printed.  If <I>c_ID[N]</I> is used, then N must be in
the range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow vector or array per-atom
quantities calculated by a <A HREF = "fix.html">fix</A> to be output.  The ID in the
keyword should be replaced by the actual ID of the fix that has been
attribute should be replaced by the actual ID of the fix that has been
defined previously in the input script.  The <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command is one that calculates per-atom
quantities.  Since it can time-average per-atom quantities produced by
@@ -346,20 +400,21 @@ any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-
<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
be written to a dump file.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
calculated by the fix is printed.  If <I>f_ID[N]</I> is used, then N must
be in the range from 1-M, which will print the Nth column of the
M-length per-atom array calculated by the fix.
</P>
<P>The <I>v_name</I> keyword allows per-atom quantities calculated by a
<A HREF = "variable.html">variable</A> to be output.  The name in the keyword should
be replaced by the actual name of the variable that has been defined
previously in the input script.  Only an atom-style variable can be
referenced, since it is the only style that generates per-atom values.
Variables of style <I>atom</I> can reference individual atom attributes,
per-atom atom attributes, thermodynamic keywords, or invoke other
computes, fixes, or variables when they are evaluated, so this is a
very general means of creating quantities to output to a dump file.
<P>If <I>f_ID</I> is used as a attribute, then the per-atom vector calculated
by the fix is printed.  If <I>f_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the fix.
</P>
<P>The <I>v_name</I> attribute allows per-atom vectors calculated by a
<A HREF = "variable.html">variable</A> to be output.  The name in the attribute
should be replaced by the actual name of the variable that has been
defined previously in the input script.  Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
values.  Variables of style <I>atom</I> can reference individual atom
attributes, per-atom atom attributes, thermodynamic keywords, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
@@ -373,10 +428,6 @@ per-atom quantities which could then be output into dump files.
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
section of the documentation.
</P>
<P>The <I>bond</I> style is part of the "molecular" package.  It is only
enabled if LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>xtc</I> style is part of the "xtc" package.  It is only enabled if
LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.  This is because
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