lammps/doc/dump.txt

"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
   
dump command :h3

[Syntax:]

dump ID group-ID style N file args :pre

ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {bond} or {dcd} or {xtc} or {xyz} or {custom} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
  {atom} args = none
  {bond} args = none
  {dcd} args = none
  {xtc} args = precision (optional)
    precision = power-of-10 value from 10 to 1000000 (default = 1000)
  {xyz} args = none
  {custom} args = list of atom attributes
    possible attributes = tag, mol, type,
			  x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
			  vx, vy, vz, fx, fy, fz,
                          q, mux, muy, muz, tqx, tqy, tqz,
		          epair, ke, etotal, centro,
                          sxx, syy, szz, sxy, sxz, syz,
			  c_ID, c_ID\[N\]
      tag = atom ID
      mol = molecule ID
      type = atom type
      x,y,z = unscaled atom coordinates
      xs,ys,zs = scaled atom coordinates
      xu,yu,zu = unwrapped atom coordinates
      ix,iy,iz = box image that the atom is in
      vx,vy,vz = atom velocities
      fx,fy,fz = forces on atoms
      q = atom charge
      mux,muy,muz = orientation of dipolar atom
      tqx,tqy,tqz = torque on dipolar atoms
      epair = per-atom pairwise energy
      ke = per-atom kinetic energy
      etotal = per-atom total energy (ke + epair)
      centro = per-atom centro-symmetry parameter
      sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
      c_ID = scalar per-atom quantity calculated by a compute identified by its ID
      c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID :pre
:ule

[Examples:]

dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz c_myF\[3\]
dump 1 all xtc 1000 file.xtc 100.0 :pre

[Description:]

Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles.  As described below, the filename
determines the kind of output (text or binary or gzipped, one big file
or one per timestep, one big file or one per processor).  Only
information for atoms in the specified group is dumped.  The
"dump_modify"_dump_modify.html command can also alter what atoms are
included.  Not all styles support all these options; see details
below.

Note that because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
written to a dump file may be slightly outside the simulation box.

Also note that when LAMMPS is running in parallel, the atom
information written to 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 {atom}, {bond}, and {custom} styles.  It is also the case
for the {xyz} style if the dump group is not {all}.  It is not the
case for the {dcd} and {xtc} styles which always write atoms in sorted
order.  So does the {xyz} style if the dump group is {all}.

:line

The {style} keyword determines what atom quantities are written to the
file and in what format.  Settings made via the
"dump_modify"_dump_modify.html command can also alter the format of
individual values and the file itself.

The {atom}, {bond}, and {custom} styles create files in a simple text
format that is self-explanatory.  Many of the LAMMPS "post-processing
tools"_Section_tools.html, including
"Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with
this format.

For style {atom}, atom coordinates are written to the file, along with
the atom ID and atom type.  By default, atom coords are written in a
scaled format (from 0 to 1).  I.e. an x value of 0.25 means the atom
is at a location 1/4 of the distance from xlo to xhi of the box
boundaries.  The format can be changed to unscaled coords via the
"dump_modify"_dump_modify.html settings.  Image flags can also be
added for each atom via dump_modify.

For style {bond}, the bond topology between atoms is written, in the
same format specified in data files read in by the
"read_data"_read_data.html 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 "bond_style"_bond_style.html command) by setting their
bond type to 0 are not written.  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.

Style {custom} 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.  Be careful not
to specify a quantity that is not defined for a particular simulation
- such as {q} for atom style {bond}, 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 some of the dump custom quantities is
given below.

The {dcd} style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages.  DCD
files are binary and thus may not be portable to different machines.
The dump group must be {all} for the {dcd} style.

The {xtc} style writes XTC files, a compressed trajectory format used
by the Gromacs molecular dynamics package, and described
"here"_http://www.gromacs.org/documentation/reference_3.3/online/xtc.html.
The precision used in XTC files can be specified; for example, a value
of 100 means that coordinates are stored to 1/100 nanometer accuracy.
XTC files are portable binary files written in the NFS XDR data
format, so that any machine which supports XDR should be able to read
them.  The dump group must be {all} for the {xtc} style.

The {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.

Note that DCD, XTC, and XYZ formatted files can be read directly by
"VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing
program).  VMD will also read LAMMPS {atom} style dump files since
someone added a LAMMPS plug-in to VMD.  I am told it requires an
initial snapshot from an XYZ formatted file to get started.

:line

Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges.  N can be changed between runs by using the
"dump_modify"_dump_modify.html command (not allowed for {dcd} style).

The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an "undump"_undump.html
command is used or when LAMMPS exits.  For the {dcd} and {xtc} styles,
this is a single large binary file.

Dump filenames can contain two wild-card characters.  If a "*"
character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
tmp.dump.20000, etc.  This option is not available for the {dcd} and
{xtc} styles.

If a "%" character appears in the filename, then one file is written
for each processor and the "%" character is replaced with the
processor ID from 0 to P-1.  For example, tmp.dump.% becomes
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc.  This creates smaller
files and can be a fast mode of output on parallel machines that
support parallel I/O for output. This option is not available for the
{dcd}, {xtc}, and {xyz} styles.

Note that the "*" and "%" characters can be used together to produce a
large number of small dump files!

If the filename ends with ".bin", the dump file (or files, if "*" or
"%" is also used) is written in binary format.  A binary dump file
will be about the same size as a text version, but will typically
write out much faster.  Of course, when post-processing, you will need
to convert it back to text format (see the "binary2txt
tool"_Section_tools.html#binary) or write your own code to read the
binary file.  The format of the binary file can be understood by
looking at the tools/binary2txt.cpp file.  This option is only
available for the {atom} and {custom} styles.

If the filename ends with ".gz", the dump file (or files, if "*" or "%"
is also used) is written in gzipped format.  A gzipped dump file will
be about 3x smaller than the text version, but will also take longer
to write.  This option is not available for the {dcd} and {xtc}
styles.

:line

This section explains the atom quantities that can be specified as
part of the {custom} style.

The {tag}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} keywords are self-explanatory.  {Tag} is the atom ID.  {Mol}
is the molecule ID, included in the data file for molecular systems.
The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the
appropriate distance units (Angstroms, sigma, etc).  Use {xs}, {ys},
{zs} if you want the coordinates "scaled" to the box size, so that
each value is 0.0 to 1.0.  Use {xu}, {yu}, {zu} if you want the
coordinates "unwrapped" by the image flags for each atom.  Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box.  Note that using {xu},
{yu}, {zu} means that the coordinate values may be far outside the box
size printed with the snapshot.  The image flags can be printed
directly using the {ix}, {iy}, {iz} keywords. The
"dump_modify"_dump_modify.html command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.

The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} keywords are specific
to dipolar systems defined with an atom style of {dipole}.  The first
3 give the orientation of the atom's dipole.  The latter 3 give the
torque on the dipolar atoms.

The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
kinetic), centro-symmetry parameter, and components of the per-atom
stress tensor for each atom.  These quantities are calculated by
computes that the dump defines, as if these commands had been issued:

compute dump-ID_epair/atom group-ID "epair/atom"_compute_epair_atom.html
compute dump-ID_ke/atom group-ID "ke/atom"_compute_ke_atom.html
compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html
compute dump-ID_centro/atom group-ID "centro/atom"_compute_centro_atom.html
compute dump-ID_stress/atom group-ID "stress/atom"_compute_stress_atom.html :pre

See the corresponding "compute"_compute.html style commands for
details on what is computed for each atom.  Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore).  The group for each new compute is the same as the dump
group.

Note that the {etotal} keyword does not include energy contributions
due to bonds, angles, etc that the atom is part of.

The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} keywords access the 6
components of the stress tensor calculated for each atom by the
"compute stress/atom"_compute_stress_atom.html style.

The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a compute to be output.  The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script.  See the
"compute"_compute.html command for details.  Note that scalar and
vector quantities that are not calculated on a per-atoms basis
(e.g. global temperature or pressure) cannot be output in a dump.
Rather, these quantities are output by the "thermo_style
custom"_thermo_style.html command.

If {c_ID} is used as a keyword, then the a single per-atom quantity
calculated by the compute is printed.  If {c_ID\[N\]} is used, then N in
the range from 1-M will print a specific component of the per-atom
vector calculated by the compute.  A value of N=0 will output the
single per-atom quantity.

See "this section"_Section_modify.html for information on how to add
new compute styles to LAMMPS that calculate per-atom quantities which
could then be output with these keywords.

:line

[Restrictions:]

To write gzipped dump files, you must compile LAMMPS with the -DGZIP
option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
documentation.

The {bond} style is part of the "molecular" package.  It is only
enabled if LAMMPS was built with that package.  See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.

The {xtc} style is part of the "xtc" package.  It is only enabled if
LAMMPS was built with that package.  See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.  This is because
some machines may not support the lo-level XDR data format that XTC
files are written with, which will result in a compile-time error when
a lo-level include file is not found.  Putting this style in a package
makes it easy to exclude from a LAMMPS build for those machines.

Granular systems and granular pair potentials cannot be used to
compute per-atom energy and stress.  The "fix
gran/diag"_fix_gran_diag.html command should be used instead.

[Related commands:]

"dump_modify"_dump_modify.html, "undump"_undump.html

[Default:] none