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< title > dump command — LAMMPS 15 May 2015 version documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< div class = "section" id = "dump-command" >
< span id = "index-0" > < / span > < h1 > dump command< a class = "headerlink" href = "#dump-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
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< div class = "section" id = "dump-h5md-command" >
< h1 > < a class = "reference internal" href = "dump_h5md.html" > < em > dump h5md< / em > < / a > command< a class = "headerlink" href = "#dump-h5md-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
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< div class = "section" id = "dump-image-command" >
< h1 > < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > command< a class = "headerlink" href = "#dump-image-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "dump-movie-command" >
< h1 > < a class = "reference internal" href = "dump_image.html" > < em > dump movie< / em > < / a > command< a class = "headerlink" href = "#dump-movie-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "dump-molfile-command" >
< h1 > < a class = "reference internal" href = "dump_molfile.html" > < em > dump molfile< / em > < / a > command< a class = "headerlink" href = "#dump-molfile-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > dump ID group-ID style N file args
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID = user-assigned name for the dump< / li >
< li > group-ID = ID of the group of atoms to be dumped< / li >
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< li > style = < em > atom< / em > or < em > atom/gz< / em > or < em > atom/mpiio< / em > or < em > cfg< / em > or < em > cfg/gz< / em > or < em > cfg/mpiio< / em > or < em > dcd< / em > or < em > xtc< / em > or < em > xyz< / em > or < em > xyz/gz< / em > or < em > xyz/mpiio< / em > or < em > h5md< / em > or < em > image< / em > or < em > movie< / em > or < em > molfile< / em > or < em > local< / em > or < em > custom< / em > or < em > custom/gz< / em > or < em > custom/mpiio< / em > < / li >
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< li > N = dump every this many timesteps< / li >
< li > file = name of file to write dump info to< / li >
< li > args = list of arguments for a particular style< / li >
< / ul >
< pre class = "literal-block" >
< em > atom< / em > args = none
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< em > atom/gz< / em > args = none
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< em > atom/mpiio< / em > args = none
< em > cfg< / em > args = same as < em > custom< / em > args, see below
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< em > cfg/gz< / em > args = same as < em > custom< / em > args, see below
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< em > cfg/mpiio< / em > args = same as < em > custom< / em > args, see below
< em > dcd< / em > args = none
< em > xtc< / em > args = none
< em > xyz< / em > args = none
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< / pre >
< pre class = "literal-block" >
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< em > xyz/gz< / em > args = none
< / pre >
< pre class = "literal-block" >
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< em > xyz/mpiio< / em > args = none
< / pre >
< pre class = "literal-block" >
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< em > h5md< / em > args = discussed on < a class = "reference internal" href = "dump_h5md.html" > < em > dump h5md< / em > < / a > doc page
< / pre >
< pre class = "literal-block" >
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< em > image< / em > args = discussed on < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page
< / pre >
< pre class = "literal-block" >
< em > movie< / em > args = discussed on < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page
< / pre >
< pre class = "literal-block" >
< em > molfile< / em > args = discussed on < a class = "reference internal" href = "dump_molfile.html" > < em > dump molfile< / em > < / a > doc page
< / pre >
< pre class = "literal-block" >
< em > local< / em > args = list of local attributes
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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
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< / pre >
< pre class = "literal-block" >
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< em > custom< / em > or < em > custom/gz< / em > or < em > custom/mpiio< / em > args = list of atom attributes
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possible attributes = id, mol, proc, procp1, 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,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
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< / pre >
< pre class = "literal-block" >
id = atom ID
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mol = molecule ID
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
element = name of atom element, as defined by < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > 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
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
d_name = per-atom floating point vector with name, managed by fix property/atom
i_name = per-atom integer vector with name, managed by fix property/atom
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > dump myDump all atom 100 dump.atom
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dump myDump all atom/mpiio 100 dump.atom.mpiio
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dump myDump all atom/gz 100 dump.atom.gz
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dump 2 subgroup atom 50 dump.run.bin
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dump 2 subgroup atom 50 dump.run.mpiio.bin
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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
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dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
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dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
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dump 1 all xtc 1000 file.xtc
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The < em > image< / em > and < em > movie< / em > styles are
the exception: the < em > image< / em > style renders a JPG, PNG, or PPM image file
of the atom configuration every N timesteps while the < em > movie< / em > style
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combines and compresses them into a movie file; both are discussed in
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detail on the < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page. The timesteps on
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which dump output is written can also be controlled by a variable.
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See the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify every< / em > < / a > command.< / p >
< p > Only information for atoms in the specified group is dumped. The
< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify thresh and region< / em > < / a > commands can also
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alter what atoms are included. Not all styles support all these
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options; see details below.< / p >
< p > As described below, the filename determines the kind of output (text
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or binary or gzipped, one big file or one per timestep, one big file
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or multiple smaller files).< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Because periodic boundary conditions are enforced only
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on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
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box.< / p >
< / div >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Unless the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify sort< / em > < / a > option
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is invoked, the lines of atom information written to dump files
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(typically one line per atom) will be in an indeterminate order for
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each snapshot. This is even true when running on a single processor,
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if the < a class = "reference internal" href = "atom_modify.html" > < em > atom_modify sort< / em > < / a > option is on, which it is
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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
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multiple processors, each of which owns a subset of the atoms.< / p >
< / div >
< p > For the < em > atom< / em > , < em > custom< / em > , < em > cfg< / em > , and < em > local< / em > styles, sorting is off by
default. For the < em > dcd< / em > , < em > xtc< / em > , < em > xyz< / em > , and < em > molfile< / em > styles, sorting by
atom ID is on by default. See the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > doc
page for details.< / p >
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< p > The < em > atom/gz< / em > , < em > cfg/gz< / em > , < em > custom/gz< / em > , and < em > xyz/gz< / em > styles are identical
in command syntax to the corresponding styles without “ gz” , however,
they generate compressed files using the zlib library. Thus the filename
suffix ” .gz” is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed network
disallows using the fork() library call (which is needed for a pipe).
For the remainder of this doc page, you should thus consider the < em > atom< / em >
and < em > atom/gz< / em > styles (etc) to be inter-changeable, with the exception
of the required filename suffix.< / p >
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< p > As explained below, the < em > atom/mpiio< / em > , < em > cfg/mpiio< / em > , < em > custom/mpiio< / em > , and
< em > xyz/mpiio< / em > styles are identical in command syntax and in the format
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of the dump files they create, to the corresponding styles without
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“ mpiio” , except the single dump file they produce is written in
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parallel via the MPI-IO library. For the remainder of this doc page,
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you should thus consider the < em > atom< / em > and < em > atom/mpiio< / em > styles (etc) to
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be inter-changeable. The one exception is how the filename is
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specified for the MPI-IO styles, as explained below.< / p >
< hr class = "docutils" / >
< p > The < em > style< / em > keyword determines what atom quantities are written to the
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file and in what format. Settings made via the
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< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > command can also alter the format of
individual values and the file itself.< / p >
< p > The < em > atom< / em > , < em > local< / em > , and < em > custom< / em > styles create files in a simple text
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format that is self-explanatory when viewing a dump file. Many of the
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LAMMPS < a class = "reference internal" href = "Section_tools.html" > < em > post-processing tools< / em > < / a > , including
< a class = "reference external" href = "http://www.sandia.gov/~sjplimp/pizza.html" > Pizza.py< / a > , work with this
format, as does the < a class = "reference internal" href = "rerun.html" > < em > rerun< / em > < / a > command.< / p >
< p > For post-processing purposes the < em > atom< / em > , < em > local< / em > , and < em > custom< / em > text
files are self-describing in the following sense.< / p >
< p > The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > ITEM: BOX BOUNDS xx yy zz
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xlo xhi
ylo yhi
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zlo zhi
< / pre > < / div >
< / div >
< p > 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
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characters that encode the style of boundary for each of the 6
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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
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< a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command for details.< / p >
< p > For triclinic simulation boxes (non-orthogonal), an orthogonal
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bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
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formatted as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > ITEM: BOX BOUNDS xy xz yz xx yy zz
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xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
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zlo_bound zhi_bound yz
< / pre > < / div >
< / div >
< p > The presence of the text “ xy xz yz” in the ITEM line indicates that
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the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
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meaning of the 6 character flags for “ xx yy zz” is the same as above.< / p >
< p > Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See < a class = "reference internal" href = "Section_howto.html#howto-12" > < span > this section< / span > < / a > of the doc pages for a geometric
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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
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parameters to and from other commonly used triclinic representations.< / p >
< p > The “ ITEM: ATOMS” line in each snapshot lists column descriptors for
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the per-atom lines that follow. For example, the descriptors would be
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“ id type xs ys zs” for the default < em > atom< / em > style, and would be the atom
attributes you specify in the dump command for the < em > custom< / em > style.< / p >
< p > For style < em > atom< / em > , atom coordinates are written to the file, along with
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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
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< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > settings. Image flags can also be
added for each atom via dump_modify.< / p >
< p > Style < em > custom< / em > allows you to specify a list of atom attributes to be
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written to the dump file for each atom. Possible attributes are
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listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation -
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such as < em > q< / em > for atom style < em > bond< / em > , since that atom style doesn’ t
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assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
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the timestep. An explanation of the possible dump custom attributes
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is given below.< / p >
< p > For style < em > local< / em > , local output generated by < a class = "reference internal" href = "compute.html" > < em > computes< / em > < / a >
and < a class = "reference internal" href = "fix.html" > < em > fixes< / em > < / a > is used to generate lines of output that is
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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
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using input from the < a class = "reference internal" href = "compute_property_local.html" > < em > compute property/local< / em > < / a > command with dump local,
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it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command.< / p >
< p > Style < em > cfg< / em > has the same command syntax as style < em > custom< / em > and writes
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extended CFG format files, as used by the
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< a class = "reference external" href = "http://mt.seas.upenn.edu/Archive/Graphics/A" > AtomEye< / a > visualization
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package. Since the extended CFG format uses a single snapshot of the
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system per file, a wildcard “ *” must be included in the filename, as
discussed below. The list of atom attributes for style < em > cfg< / em > must
begin with either “ mass type xs ys zs” or “ mass type xsu ysu zsu”
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since these quantities are needed to write the CFG files in the
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appropriate format (though the “ mass” and “ type” fields do not appear
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explicitly in the file). Any remaining attributes will be stored as
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“ auxiliary properties” in the CFG files. Note that you will typically
want to use the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify element< / em > < / a > command with
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CFG-formatted files, to associate element names with atom types, so
that AtomEye can render atoms appropriately. When unwrapped
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coordinates < em > xsu< / em > , < em > ysu< / em > , and < em > zsu< / em > are requested, the nominal AtomEye
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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
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unaffected.< / p >
< p > The < em > dcd< / em > style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines.
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The number of atoms per snapshot cannot change with the < em > dcd< / em > style.
The < em > unwrap< / em > option of the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > command
allows DCD coordinates to be written “ unwrapped” by the image flags
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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
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the box size stored with the snapshot.< / p >
< p > The < em > xtc< / em > style writes XTC files, a compressed trajectory format used
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by the GROMACS molecular dynamics package, and described
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< a class = "reference external" href = "http://manual.gromacs.org/current/online/xtc.html" > here< / a > .
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The precision used in XTC files can be adjusted via the
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< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > command. The default value of 1000
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means that coordinates are stored to 1/1000 nanometer accuracy. XTC
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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 < em > xtc< / em > style.
The < em > unwrap< / em > option of the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > command allows
XTC coordinates to be written “ unwrapped” by the image flags for each
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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
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stored with the snapshot.< / p >
< p > The < em > xyz< / em > style writes XYZ files, which is a simple text-based
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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
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< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify element< / em > < / a > option to change the output
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from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
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bonds and colors.< / p >
< p > Note that < em > atom< / em > , < em > custom< / em > , < em > dcd< / em > , < em > xtc< / em > , and < em > xyz< / em > style dump files
can be read directly by < a class = "reference external" href = "http://www.ks.uiuc.edu/Research/vmd" > VMD< / a > , a
popular molecular viewing program. See < a class = "reference internal" href = "Section_tools.html#vmd" > < span > Section tools< / span > < / a > of the manual and the
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tools/lmp2vmd/README.txt file for more information about support in
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VMD for reading and visualizing LAMMPS dump files.< / p >
< hr class = "docutils" / >
< p > Dumps are performed on timesteps that are a multiple of N (including
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timestep 0) and on the last timestep of a minimization if the
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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
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changed via the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify first< / em > < / a > command, which
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can also be useful if the dump command is invoked after a minimization
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ended on an arbitrary timestep. N can be changed between runs by
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using the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify every< / em > < / a > command (not allowed
for < em > dcd< / em > style). The < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify every< / em > < / a > command
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also allows a variable to be used to determine the sequence of
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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
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< a class = "reference internal" href = "dump_modify.html" > < em > dump_modify first< / em > < / a > command is used.< / p >
< p > The specified filename determines how the dump file(s) is written.
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The default is to write one large text file, which is opened when the
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dump command is invoked and closed when an < a class = "reference internal" href = "undump.html" > < em > undump< / em > < / a >
command is used or when LAMMPS exits. For the < em > dcd< / em > and < em > xtc< / em > styles,
this is a single large binary file.< / p >
< p > Dump filenames can contain two wildcard characters. If a “ *”
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character appears in the filename, then one file per snapshot is
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written and the “ *” character is replaced with the timestep value.
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For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
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tmp.dump.20000, etc. This option is not available for the < em > dcd< / em > and
< em > xtc< / em > styles. Note that the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify pad< / em > < / a >
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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
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in order with some post-processing tools.< / p >
< p > If a “ %” character appears in the filename, then each of P processors
writes a portion of the dump file, and the “ %” character is replaced
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with the processor ID from 0 to P-1. For example, tmp.dump.% becomes
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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
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< em > dcd< / em > , < em > xtc< / em > , and < em > xyz< / em > styles.< / p >
< p > By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the < em > nfile< / em > or
< em > fileper< / em > keywords of the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > command.
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These options can be the most efficient way of writing out dump files
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when running on large numbers of processors.< / p >
< p > Note that using the “ *” and “ %” characters together can produce a
large number of small dump files!< / p >
< p > For the < em > atom/mpiio< / em > , < em > cfg/mpiio< / em > , < em > custom/mpiio< / em > , and < em > xyz/mpiio< / em >
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styles, a single dump file is written in parallel via the MPI-IO
library, which is part of the MPI standard for versions 2.0 and above.
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
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package installed, e.g.< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform
< / pre > < / div >
< / div >
< p > Second, use a dump filename which contains ” .mpiio” . Note that it
does not have to end in ” .mpiio” , just contain those characters.
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Unlike MPI-IO restart files, which must be both written and read using
MPI-IO, the dump files produced by these MPI-IO styles are identical
in format to the files produced by their non-MPI-IO style
counterparts. This means you can write a dump file using MPI-IO and
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use the < a class = "reference internal" href = "read_dump.html" > < em > read_dump< / em > < / a > command or perform other
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post-processing, just as if the dump file was not written using
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MPI-IO.< / p >
< p > Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the “ %” wildcard character described
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above in the filename since that specifies generation of multiple
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files. You can use the ” .bin” suffix described below in an MPI-IO
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dump file; again this file will be written in parallel and have the
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same binary format as if it were written without MPI-IO.< / p >
< p > 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
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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
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to convert it back to text format (see the < a class = "reference internal" href = "Section_tools.html#binary" > < span > binary2txt tool< / span > < / a > ) or write your own code to read the
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binary file. The format of the binary file can be understood by
looking at the tools/binary2txt.cpp file. This option is only
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available for the < em > atom< / em > and < em > custom< / em > styles.< / p >
< p > If the filename ends with ” .gz” , the dump file (or files, if “ *” or “ %”
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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
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to write. This option is not available for the < em > dcd< / em > and < em > xtc< / em >
styles.< / p >
< hr class = "docutils" / >
< p > This section explains the local attributes that can be specified as
part of the < em > local< / em > style.< / p >
< p > The < em > index< / em > attribute can be used to generate an index number from 1
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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
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snapshots.< / p >
< p > The < em > c_ID< / em > and < em > c_ID[N]< / em > attributes allow local vectors or arrays
calculated by a < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > to be output. The ID in the
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attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
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< a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command for details. There are computes for
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calculating local information such as indices, types, and energies for
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bonds and angles.< / p >
< p > Note that computes which calculate global or per-atom quantities, as
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opposed to local quantities, cannot be output in a dump local command.
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Instead, global quantities can be output by the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > command, and per-atom quantities can be
output by the dump custom command.< / p >
< p > If < em > c_ID< / em > is used as a attribute, then the local vector calculated by
the compute is printed. If < em > c_ID[N]< / em > is used, then N must be in the
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range from 1-M, which will print the Nth column of the M-length local
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array calculated by the compute.< / p >
< p > The < em > f_ID< / em > and < em > f_ID[N]< / em > attributes allow local vectors or arrays
calculated by a < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > to be output. The ID in the attribute
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should be replaced by the actual ID of the fix that has been defined
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previously in the input script.< / p >
< p > If < em > f_ID< / em > is used as a attribute, then the local vector calculated by
the fix is printed. If < em > f_ID[N]< / em > is used, then N must be in the
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range from 1-M, which will print the Nth column of the M-length local
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array calculated by the fix.< / p >
< p > Here is an example of how to dump bond info for a system,
including the distance and energy of each bond:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all property/local batom1 batom2 btype
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compute 2 all bond/local dist eng
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dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
< / pre > < / div >
< / div >
< hr class = "docutils" / >
< p > This section explains the atom attributes that can be specified as
part of the < em > custom< / em > and < em > cfg< / em > styles.< / p >
< p > The < em > id< / em > , < em > mol< / em > , < em > proc< / em > , < em > procp1< / em > , < em > type< / em > , < em > element< / em > , < em > mass< / em > , < em > vx< / em > ,
< em > vy< / em > , < em > vz< / em > , < em > fx< / em > , < em > fy< / em > , < em > fz< / em > , < em > q< / em > attributes are self-explanatory.< / p >
< p > < em > Id< / em > is the atom ID. < em > Mol< / em > is the molecule ID, included in the data
file for molecular systems. < em > Proc< / em > is the ID of the processor (0 to
Nprocs-1) that currently owns the atom. < em > Procp1< / em > is the proc ID+1,
which can be convenient in place of a < em > type< / em > attribute (1 to Ntypes)
for coloring atoms in a visualization program. < em > Type< / em > is the atom
type (1 to Ntypes). < em > Element< / em > is typically the chemical name of an
element, which you must assign to each type via the < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify element< / em > < / a > command. More generally, it can be any
string you wish to associated with an atom type. < em > Mass< / em > is the atom
mass. < em > Vx< / em > , < em > vy< / em > , < em > vz< / em > , < em > fx< / em > , < em > fy< / em > , < em > fz< / em > , and < em > q< / em > are components of
atom velocity and force and atomic charge.< / p >
< p > There are several options for outputting atom coordinates. The < em > x< / em > ,
< em > y< / em > , < em > z< / em > attributes write atom coordinates “ unscaled” , in the
appropriate distance < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > (Angstroms, sigma, etc). Use
< em > xs< / em > , < em > ys< / em > , < em > zs< / em > if you want the coordinates “ scaled” to the box size,
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so that each value is 0.0 to 1.0. If the simulation box is triclinic
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(tilted), then all atom coords will still be between 0.0 and 1.0. Use
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< em > xu< / em > , < em > yu< / em > , < em > zu< / em > if you want the coordinates “ unwrapped” by the image
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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
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periodic box. Note that using < em > xu< / em > , < em > yu< / em > , < em > zu< / em > means that the
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coordinate values may be far outside the box bounds printed with the
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snapshot. Using < em > xsu< / em > , < em > ysu< / em > , < em > zsu< / em > is similar to using < em > xu< / em > , < em > yu< / em > , < em > zu< / em > ,
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except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
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cooordinate increased or decreased by 1.0.< / p >
< p > The image flags can be printed directly using the < em > ix< / em > , < em > iy< / em > , < em > iz< / em >
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attributes. For periodic dimensions, they specify which image of the
simulation box the atom is considered to be in. 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
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periodic boundaries during the simulation.< / p >
< p > The < em > mux< / em > , < em > muy< / em > , < em > muz< / em > attributes are specific to dipolar systems
defined with an atom style of < em > dipole< / em > . They give the orientation of
the atom’ s point dipole moment. The < em > mu< / em > attribute gives the
magnitude of the atom’ s dipole moment.< / p >
< p > The < em > radius< / em > and < em > diameter< / em > attributes are specific to spherical
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particles that have a finite size, such as those defined with an atom
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style of < em > sphere< / em > .< / p >
< p > The < em > omegax< / em > , < em > omegay< / em > , and < em > omegaz< / em > attributes are specific to
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finite-size spherical particles that have an angular velocity. Only
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certain atom styles, such as < em > sphere< / em > define this quantity.< / p >
< p > The < em > angmomx< / em > , < em > angmomy< / em > , and < em > angmomz< / em > attributes are specific to
2013-02-01 08:24:05 +08:00
finite-size aspherical particles that have an angular momentum. Only
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the < em > ellipsoid< / em > atom style defines this quantity.< / p >
< p > The < em > tqx< / em > , < em > tqy< / em > , < em > tqz< / em > attributes are for finite-size particles that
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can sustain a rotational torque due to interactions with other
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particles.< / p >
< p > The < em > c_ID< / em > and < em > c_ID[N]< / em > attributes allow per-atom vectors or arrays
calculated by a < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > to be output. The ID in the
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attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
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< a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command for details. There are computes for
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calculating the per-atom energy, stress, centro-symmetry parameter,
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and coordination number of individual atoms.< / p >
< p > Note that computes which calculate global or local quantities, as
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opposed to per-atom quantities, cannot be output in a dump custom
command. Instead, global quantities can be output by the
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< a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > command, and local quantities
can be output by the dump local command.< / p >
< p > If < em > c_ID< / em > is used as a attribute, then the per-atom vector calculated
by the compute is printed. If < em > c_ID[N]< / em > is used, then N must be in
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the range from 1-M, which will print the Nth column of the M-length
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per-atom array calculated by the compute.< / p >
< p > The < em > f_ID< / em > and < em > f_ID[N]< / em > attributes allow vector or array per-atom
quantities calculated by a < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > to be output. The ID in the
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attribute should be replaced by the actual ID of the fix that has been
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defined previously in the input script. The < a class = "reference internal" href = "fix_ave_atom.html" > < em > fix ave/atom< / em > < / a > command is one that calculates per-atom
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quantities. Since it can time-average per-atom quantities produced by
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any < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > , < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > , or atom-style
< a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > , this allows those time-averaged results to
be written to a dump file.< / p >
< p > If < em > f_ID< / em > is used as a attribute, then the per-atom vector calculated
by the fix is printed. If < em > f_ID[N]< / em > is used, then N must be in the
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range from 1-M, which will print the Nth column of the M-length
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per-atom array calculated by the fix.< / p >
< p > The < em > v_name< / em > attribute allows per-atom vectors calculated by a
< a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > to be output. The name in the attribute
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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
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values. Variables of style < em > atom< / em > can reference individual atom
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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
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dump file.< / p >
< p > The < em > d_name< / em > and < em > i_name< / em > attributes allow to output custom per atom
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floating point or integer properties that are managed by
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< a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > .< / p >
< p > See < a class = "reference internal" href = "Section_modify.html" > < em > Section_modify< / em > < / a > of the manual for information
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on how to add new compute and fix styles to LAMMPS to calculate
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per-atom quantities which could then be output into dump files.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
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< p > To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package
- see the < a class = "reference internal" href = "Section_start.html#start-2" > < span > Making LAMMPS< / span > < / a > section of
the documentation.< / p >
< p > The < em > atom/gz< / em > , < em > cfg/gz< / em > , < em > custom/gz< / em > , and < em > xyz/gz< / em > styles are part
of the COMPRESS package. They are only enabled if LAMMPS was built
with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
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< p > The < em > atom/mpiio< / em > , < em > cfg/mpiio< / em > , < em > custom/mpiio< / em > , and < em > xyz/mpiio< / em > styles
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are part of the MPIIO package. They are only enabled if LAMMPS was
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built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > The < em > xtc< / em > style is part of the XTC package. It is only enabled if
LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info. This is
2011-08-26 00:46:23 +08:00
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
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machines.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
2015-08-19 23:38:41 +08:00
< p > < a class = "reference internal" href = "dump_h5md.html" > < em > dump h5md< / em > < / a > , < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > ,
< a class = "reference internal" href = "dump_molfile.html" > < em > dump molfile< / em > < / a > , < a class = "reference internal" href = "dump_modify.html" > < em > dump_modify< / em > < / a > ,
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< a class = "reference internal" href = "undump.html" > < em > undump< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The defaults for the < em > image< / em > and < em > movie< / em > styles are listed on the
< a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page.< / p >
< / div >
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