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"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
"dump image"_dump_image.html command :h3
"dump molfile"_dump_molfile.html 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 {cfg} or {dcd} or {xtc} or {xyz} or {image} or {molfile} or {local} 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
{cfg} args = same as {custom} args, see below
{dcd} args = none
{xtc} args = none
{xyz} args = none :pre
{image} args = discussed on "dump image"_dump_image.html doc page :pre
{molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
{local} 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
{custom} args = list of atom attributes
possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID
type = atom type
element = name of atom element, as defined by "dump_modify"_dump_modify.html command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled 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 dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
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 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
:ule
[Examples:]
dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre
[Description:]
Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The {image} style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the "dump
image"_dump_image.html doc page. The timesteps on which dump output
is written can also be controlled by a variable. See the "dump_modify
every"_dump_modify.html command.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also
alter what atoms are included. Not all styles support all these
options; see details below.
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).
IMPORTANT NOTE: 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.
IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
is invoked, the lines of atom information written to dump files
(typically one line per atom) will be in an indeterminate order for
each snapshot. This is even true when running on a single processor,
if the "atom_modify sort"_atom_modify.html option is on, which it is
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors.
For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
atom ID is on by default. See the "dump_modify"_dump_modify.html doc
page for details.
: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}, {local}, and {custom} styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS "post-processing tools"_Section_tools.html, including
"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this
format, as does the "rerun"_rerun.html command.
For post-processing purposes the {atom}, {local}, and {custom} text
files are self-describing in the following sense.
The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:
ITEM: BOX BOUNDS xx yy zz
xlo xhi
ylo yhi
zlo zhi :pre
where xlo,xhi are the maximum extents of the simulation box in the
x-dimension, and similarly for y and z. The "xx yy zz" represent 6
characters that encode the style of boundary for each of the 6
simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
or m = shrink wrapped with a minimum value. See the
"boundary"_boundary.html command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:
ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz :pre
The presence of the text "xy xz yz" in the ITEM line indicates that
the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
calculated from the triclinic parameters, and how to transform those
parameters to and from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
"id type xs ys zs" for the default {atom} style, and would be the atom
attributes you specify in the dump command for the {custom} style.
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.
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. You cannot
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 the possible dump custom attributes
is given below.
For style {local}, local output generated by "computes"_compute.html
and "fixes"_fix.html is used to generate 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 "compute
property/local"_compute_property_local.html 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
"read_data"_read_data.html command.
Style {cfg} has the same command syntax as style {custom} and writes
extended CFG format files, as used by the
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wildcard "*" must be included in the filename, as
discussed below. The list of atom attributes for style {cfg} must
begin with either "id type xs ys zs" or "id type xsu ysu zsu" or
since these quantities are needed to
write the CFG files in the appropriate format (though the "id" and
"type" fields do not appear explicitly in the file). Any remaining
attributes will be stored as "auxiliary properties" in the CFG files.
Note that you will typically want to use the "dump_modify
element"_dump_modify.html command with CFG-formatted files, to
associate element names with atom types, so that AtomEye can render
atoms appropriately. When unwrapped coordinates {xsu}, {ysu}, and {zsu}
are requested, the nominal AtomEye periodic cell dimensions are expanded
by a large factor UNWRAPEXPAND = 10.0, which ensures atoms that are
displayed correctly for up to UNWRAPEXPAND/2 periodic boundary crossings
in any direction.
Beyond this, AtomEye will rewrap the unwrapped coordinates.
The expansion causes the atoms to be drawn farther
away from the viewer, but it is easy to zoom the atoms closer, and
the interatomic distances are unaffected.
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 number of atoms per snapshot cannot change with the {dcd} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command
allows DCD coordinates to be written "unwrapped" by the image flags
for each atom. Unwrapped means that if the atom has passed through
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 these coordinates may thus be far outside
the box size stored with the snapshot.
The {xtc} style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
"here"_http://manual.gromacs.org/current/online/xtc.html.
The precision used in XTC files can be adjusted via the
"dump_modify"_dump_modify.html command. The default value of 1000
means that coordinates are stored to 1/1000 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 number of atoms per snapshot cannot change with the {xtc} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command allows
XTC coordinates to be written "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 these coordinates may thus be far outside the box size
stored with the snapshot.
The {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read. Specifically it has
a line with the number of atoms, then a comment line that is
usually ignored followed by one line per atom with the atom type
and the x-, y-, and z-coordinate of that atom. You can use the
"dump_modify element"_dump_modify.html option to change the output
from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
bonds and colors.
Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files can
be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular
molecular viewing program). See "Section tools"_Section_tools.html#vmd
of the manual and the tools/lmp2vmd/README.txt file for more information
about support in VMD for reading and visualizing LAMMPS dump files.
: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. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command (not allowed
for {dcd} style). The "dump_modify every"_dump_modify.html command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
"dump_modify first"_dump_modify.html command is used.
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 wildcard 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. Note that the "dump_modify pad"_dump_modify.html
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order by some post-processing tools.
If a "%" character appears in the filename, then each of P processors
writes a portion of the dump file, 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.
By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the {nfile} or
{fileper} keywords of the "dump_modify"_dump_modify.html command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.
Note that using the "*" and "%" characters together can 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 local attributes that can be specified as
part of the {local} style.
The {index} 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.
The {c_ID} and {c_ID\[N\]} attributes allow local vectors or arrays
calculated by a "compute"_compute.html 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
"compute"_compute.html command for details. There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
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 "thermo_style
custom"_thermo_style.html command, and per-atom quantities can be
output by the dump custom command.
If {c_ID} is used as a attribute, then the local vector calculated by
the compute is printed. If {c_ID\[N\]} 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.
The {f_ID} and {f_ID\[N\]} attributes allow local vectors or arrays
calculated by a "fix"_fix.html 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.
If {f_ID} is used as a attribute, then the local vector calculated by
the fix is printed. If {f_ID\[N\]} 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.
Here is an example of how to dump bond info for a system,
including the distance and energy of each bond:
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre
:line
This section explains the atom attributes that can be specified as
part of the {custom} and {cfg} styles.
The {id}, {mol}, {type}, {element}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} attributes are self-explanatory.
{Id} is the atom ID. {Mol} is the molecule ID, included in the data
file for molecular systems. {Type} is the atom type. {Element} is
typically the chemical name of an element, which you must assign to
each type via the "dump_modify element"_dump_modify.html command.
More generally, it can be any string you wish to associated with an
atom type. {Mass} is the atom mass. {Vx}, {vy}, {vz}, {fx}, {fy},
{fz}, and {q} are components of atom velocity and force and atomic
charge.
There are several options for outputting atom coordinates. The {x},
{y}, {z} attributes write atom coordinates "unscaled", in the
appropriate distance "units"_units.html (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. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 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 bounds printed with the
snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu},
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix},
{iy}, {iz} attributes. 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} attributes are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of
the atom's point dipole moment. The {mu} attribute gives the
magnitude of the atom's dipole moment.
The {radius} and {diameter} attributes are specific to spherical
particles that have a finite size, such as those defined with an atom
style of {sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to
finite-size spherical particles that have an angular velocity. Only
certain atom styles, such as {sphere} define this quantity.
The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
finite-size aspherical particles that have an angular momentum. Only
the {ellipsoid} atom style defines this quantity.
The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
can sustain a rotational torque due to interactions with other
particles.
The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See "atom_style
electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
details.
The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
calculated by a "compute"_compute.html 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
"compute"_compute.html command for details. There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.
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
"thermo_style custom"_thermo_style.html command, and local quantities
can be output by the dump local command.
If {c_ID} is used as a attribute, then the per-atom vector calculated
by the compute is printed. If {c_ID\[N\]} 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.
The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
quantities calculated by a "fix"_fix.html 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. The "fix
ave/atom"_fix_ave_atom.html command is one that calculates per-atom
quantities. Since it can time-average per-atom quantities produced by
any "compute"_compute.html, "fix"_fix.html, or atom-style
"variable"_variable.html, this allows those time-averaged results to
be written to a dump file.
If {f_ID} is used as a attribute, then the per-atom vector calculated
by the fix is printed. If {f_ID\[N\]} 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.
The {v_name} attribute allows per-atom vectors calculated by a
"variable"_variable.html 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 {atom} 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.
See "Section_modify"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
:line
[Restrictions:]
To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
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#start_3 section for more info. This is
because some machines may not support the low-level XDR data format
that XTC files are written with, which will result in a compile-time
error when a low-level include file is not found. Putting this style
in a package makes it easy to exclude from a LAMMPS build for those
machines. However, the XTC package also includes two compatibility
header files and associated functions, which should be a suitable
substitute on machines that do not have the appropriate native header
files. This option can be invoked at build time by adding
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
machines and should also work on IBM BG/P, and Windows XP/Vista/7
machines.
[Related commands:]
"dump image"_dump_image.html, "dump_modify"_dump_modify.html,
"undump"_undump.html
[Default:]
The defaults for the image style are listed on the "dump
image"_dump_image.html doc page.
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