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lammps/doc/dump.txt

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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
[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 = none
{xyz} args = none
{custom} args = list of atom attributes
possible attributes = id, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name
id = 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
radius = radius of extended spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
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 scalar value calculated by a compute with ID
c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value 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 1 all xtc 1000 file.xtc :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.
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.
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 when viewing a dump file. 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 post-processing purposes the {atom} and {custom} text files are
self-describing in the following sense. The simulation box bounds are
included in each snapshot and if the box is triclinic
(non-orthogonal), then the tilt factors are also printed; see the
"region prism"_region.html command for a description of tilt factors.
For triclinic boxes the box bounds themselves (first 2 quantities on
each line) are a true "bounding box" around the simulation domain,
which means they include the effect of any tilt. The "ITEM: ATOMS"
line in each snapshot also lists the meaning of each column of the
per-atom lines that follow. For example, this would be "id type xs ys
zs" for the default {atom} style, and it will 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.
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. 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 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 {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 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 {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 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
dump group must be {all} for 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.
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). We are told VMD will also read LAMMPS {atom} style dump
files since someone has added a LAMMPS format plug-in to VMD. It may
require 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 {id}, {mol}, {type}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} keywords 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. {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} keywords 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 simluation 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 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} keywords are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of
the atom's point dipole moment.
The {radius} keyword is specific to extended spherical particles
that have a finite size, such as granular particles defined with
an atom style of {granular}.
The {omegax}, {omegay}, and {omegaz} keywords are specific to extended
spherical or aspherical particles that have an angular velocity. Only
certain atom styles, such as {granular} or {dipole} define this
quantity.
The {angmomx}, {angmomy}, and {angmomz} keywords are specific to
extended aspherical particles that have an angular momentum. Only
the {ellipsoid} atom style defines this quantity.
The {quatw}, {quati}, {quatj}, {quatk} keywords are for aspherical
particles defined with an atom style of {ellipsoid}. They are the
components of the quaternion that defines the orientation of the
particle.
The {tqx}, {tqy}, {tqz} keywords are for extended spherical or
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a "compute"_compute.html 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
"compute"_compute.html command for details. There are per-atom
computes for calculating the energy, stress, centro-symmetry
parameter, and coordination number of individual atoms.
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 "thermo_style
custom"_thermo_style.html command.
If {c_ID} is used as a keyword, then the scalar per-atom quantity
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 component of
the M-length per-atom vector calculated by the compute.
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a "fix"_fix.html to be output. The ID in the
keyword 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 keyword, then the scalar per-atom quantity
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 component of the
M-length per-atom vector calculated by the fix.
The {v_name} keyword allows per-atom quantities calculated by a
"variable"_variable.html 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 {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 "this section"_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#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_3 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_3 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.
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 lo-level Makefile,
e.g. src/MAKE/Makefile.foo. This compatibility mode has been tested
successfully on Cray XT3 and IBM BlueGene/L machines and should also
work on the Cray XT4, IBM BG/P, and Windows XP machines.
[Related commands:]
"dump_modify"_dump_modify.html, "undump"_undump.html
[Default:] none
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