LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands

### dump command

### dump image command

Syntax:

    dump ID group-ID style N file args

- ID = user-assigned name for the dump
- group-ID = ID of the group of atoms to be dumped
- style = atom or cfg or dcd or xtc or xyz or image or local or custom
- N = dump every this many timesteps
- file = name of file to write dump info to
- args = list of arguments for a particular style

        atom args = none
        cfg args = same as custom args, see below
        dcd args = none
        xtc args = none
        xyz args = none

        image args = discussed on dump image doc page

        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

        custom args = list of atom attributes
          possible attributes = id, mol, type, 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, 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

            id = atom ID
            mol = molecule ID
            type = atom type
            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 = radius of spherical particle
            omegax,omegay,omegaz = angular velocity of extended particle
            angmomx,angmomy,angmomz = angular momentum of extended particle
            tqx,tqy,tqz = torque on extended 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

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_Stress2
    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

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 doc page.

Only information for atoms in the specified group is dumped. The dump_modify thresh and region 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 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 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, and xyz styles, sorting by atom ID is on by default. See the dump_modify doc page for details.

The style keyword determines what atom quantities are written to the file and in what format. Settings made via the dump_modify 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, including Pizza.py, work with this format.

For post-processing purposes the atom 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

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 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

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 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 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 and fixes is used to gnerate lines of output that is written to the dump file. This local data is typically calculated by each processor based on the atoms it owns, but there may be zero or more entities per atom, e.g. a list of bond distances. An explanation of the possible dump local attributes is given below. Note that by using input from the compute property/local 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 command.

Style cfg has the same command syntax as style custom and writes extended CFG format files, as used by the AtomEye 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 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 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. The precision used in XTC files can be adjusted via the dump_modify 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 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 (a popular molecular viewing program). See this section of the manual and the tools/lmp2vmd/README.txt file for more information about support in VMD for reading and visualizing LAMMPS dump files.

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 command, which can 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 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 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 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 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) 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.

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 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 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 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 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.

This section explains the atom attributes that can be specified as part of the custom and cfg styles.

The id, mol, type, 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. 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 (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 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 attribute is specific to extended 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 extended spherical or aspherical 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 extended aspherical particles that have an angular momentum. Only the ellipsoid atom style defines this quantity.

The tqx, tqy, tqz attributes are for extended spherical or aspherical 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 and pair_style eff for more details.

The c_ID and c_ID[N] attributes allow per-atom vectors or arrays calculated by a compute 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 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 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 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 command is one that calculates per-atom quantities. Since it can time-average per-atom quantities produced by any compute, fix, or atom-style variable, 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 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 this section 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.

Restrictions:

To write gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the Making LAMMPS 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 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_modify, undump

Default:

The defaults for the image style are listed on the dump image doc page.