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### dump 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 bond or dcd or xtc or xyz 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
        bond args = none
        dcd args = none
        xtc args = precision (optional)
          precision = power-of-10 value from 10 to 1000000 (default = 1000)
        xyz args = none
        custom args = list of atom attributes
          possible attributes = tag, mol, type,
      			  x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
      			  vx, vy, vz, fx, fy, fz,
                                q, mux, muy, muz,
      			  quatw, quati, quatj, quatk, tqx, tqy, tqz,
      			  c_ID, c_ID[N], f_ID, f_ID[N]
            tag = atom ID
            mol = molecule ID
            type = atom type
            x,y,z = unscaled atom coordinates
            xs,ys,zs = scaled atom coordinates
            xu,yu,zu = unwrapped atom coordinates
            ix,iy,iz = box image that the atom is in
            vx,vy,vz = atom velocities
            fx,fy,fz = forces on atoms
            q = atom charge
            mux,muy,muz = orientation of dipolar atom
            quatw,quati,quatj,quatk = quaternion components for aspherical particles
            tqx,tqy,tqz = torque on aspherical particles
            c_ID = scalar per-atom quantity calculated by a compute identified by its ID
            c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
            f_ID = scalar per-atom quantity calculated by a fix identified by its ID
            f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID

Examples:

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

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 command can also alter what atoms are included. Not all styles support all these options; see details below.

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

Also note that when LAMMPS is running in parallel, the atom information written to dump files (typically one line per atom) may be written in an indeterminate order. This is because data for a single snapshot is collected from multiple processors. This is always the case for the atom, bond, and custom styles. It is also the case for the xyz style if the dump group is not all. It is not the case for the dcd and xtc styles which always write atoms in sorted order. So does the xyz style if the dump group is all.

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, 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, including Pizza.py, work with this format.

For style atom, atom coordinates are written to the file, along with the atom ID and atom type. By default, atom coords are written in a scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom is at a location 1/4 of the distance from xlo to xhi of the box boundaries. The format can be changed to unscaled coords via the dump_modify 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 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 command) by setting their bond type to 0 are not written. Bonds that have been turned off (see the fix shake or delete_bonds commands) by setting their bond type negative are written into the file.

Style custom allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. Be careful not to specify a quantity that is not defined for a particular simulation - such as q for atom style bond, since that atom style doesn't assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the dump custom quantities is given below.

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

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

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

Note that DCD, XTC, and XYZ formatted files can be read directly by VMD (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.

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 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 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) 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 atom quantities that can be specified as part of the custom style.

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

The quatw, quati, quatj, quatk, tqx, tqy, tqz keywords are specific to aspherical particles defined with an atom style of ellipsoid. The first 4 are the components of the quaternion that define the orientiation of the particle. The final 3 give the rotational torque on the particle.

The c_ID and c_ID[N] keywords allow scalar or vector per-atom quantities calculated by a compute to be output. The ID in the keyword should be replaced by the actual ID of the compute that has been defined previously in the input script. See the compute command for details. There are pre-defined computes for calculating the energy, stress, centro-symmetry parameter, and coordination number of individual atoms. The "compute variable/atom" command will evaluate a per-atom formula you define via the variable atom command, for each atom, which can then be dumped.

Note that scalar and vector quantities that are not calculated on a per-atom basis by a compute (e.g. global temperature or pressure) cannot be output in a dump. Rather, these quantities can be output by the thermo_style custom 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 in the range from 1-M 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 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. Currently the fix ave/atom command is the only fix that calculates per-atom quantities. Since it takes a per-atom compute as an argument it effectively time-averages any of the previously described compute quantities so the time-averaged result can 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 in the range from 1-M will print the Nth component of the M-length per-atom vector calculated by the fix.

See this section of the manual for information on how to add new compute and fix styles to LAMMPS that calculate per-atom quantities which could then be output with these keywords.

Restrictions:

Scaled coordinates cannot be writted to dump files when the simulation box is triclinic (non-orthogonal). Note that this is the default for dump style atom; the dump_modify command must be used to change it. The exception is DCD files which store the tilt factors for subsequent visualization by programs like VMD.

To write gzipped dump files, you must compile LAMMPS with the -DGZIP option - see the Making LAMMPS 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 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 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.

Some pair potentials do not allow the calculation of per-atom energy and stress via the epair, etotal, sxx, etc keywords. One of these are the granular pair potentials. However, for those potentials, the fix gran/diag command can be used instead.

Related commands:

dump_modify, undump

Default: none