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326 lines
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>read_dump command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>read_dump file Nstep field1 field2 ... keyword values ...
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</PRE>
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<UL><LI>file = name of dump file to read
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<LI>Nstep = snapshot timestep to read from file
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<LI>one or more fields may be appended
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<PRE>field = <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>ix</I> or <I>iy</I> or <I>iz</I>
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<I>x</I>,<I>y</I>,<I>z</I> = atom coordinates
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<I>vx</I>,<I>vy</I>,<I>vz</I> = velocity components
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<I>ix</I>,<I>iy</I>,<I>iz</I> = image flags in each dimension
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>box</I> or <I>replace</I> or <I>purge</I> or <I>trim</I> or <I>add</I> or <I>label</I> or <I>scaled</I> or <I>format</I>
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<PRE> <I>box</I> value = <I>yes</I> or <I>no</I> = replace simulation box with dump box
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<I>replace</I> value = <I>yes</I> or <I>no</I> = overwrite atoms with dump atoms
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<I>purge</I> value = <I>yes</I> or <I>no</I> = delete all atoms before adding dump atoms
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<I>trim</I> value = <I>yes</I> or <I>no</I> = trim atoms not in dump snapshot
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<I>add</I> value = <I>yes</I> or <I>no</I> = add new dump atoms to system
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<I>label</I> value = field column
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field = one of the listed fields or <I>id</I> or <I>type</I>
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column = label on corresponding column in dump file
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<I>scaled</I> value = <I>yes</I> or <I>no</I> = coords in dump file are scaled/unscaled
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<I>format</I> values = format of dump file, must be last keyword if used
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<I>native</I> = native LAMMPS dump file
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<I>xyz</I> = XYZ file
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<I>molfile</I> style path = VMD molfile plugin interface
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style = <I>dcd</I> or <I>xyz</I> or others supported my mofile
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path = optional path for location of molfile plugins
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>read_dump dump.file 5000 x y z
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read_dump dump.xyz 5 x y z format xyz box no
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read_dump dump.xyz 10 x y z format molfile box no reader xyz "../plugins"
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read_dump dump.dcd 0 x y z format molfile box yes reader dcd
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read_dump dump.file 1000 x y z vx vy vz format molfile box yes reader lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
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read_dump dump.file 5000 x y vx vy trim yes
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read_dump ../run7/dump.file.gz 10000 x y z box yes
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read_dump dump.xyz 5 x y z box no format xyz
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read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
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read_dump dump.dcd 0 x y z format molfile dcd
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read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Read atom information from a dump file to overwrite the current atom
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coordinates, and optionally the atom velocities and image flags and
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the simluation box dimensions. This is useful for restarting a run
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from a particular snapshot in a dump file. See the
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<A HREF = "read_restart.html">read_restart</A> and <A HREF = "read_data.html">read_data</A>
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commands and the <A HREF = "Section_tools.html#restart">restart2data</A> tool for
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alternative methods to do this. Also see the <A HREF = "rerun.html">rerun</A>
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command for a means of reading multiple snapshots from a dump file.
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</P>
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<P>Note that a simulation box must already be defined before using the
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read_dump command. This can be done by the
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<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
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<A HREF = "read_restart.html">read_restart</A> commands. The read_dump command can
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reset the simulation box dimensions, as explained below.
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</P>
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<P>Also note that reading per-atom information from a dump snapshot is
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limited to the atom coordinates, velocities and image flags, as
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explained below. Other atom properties, which may be necessary to run
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a valid simulation, such as atom charge, or bond topology information
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for a molecular system, are not read from (or even contained in) dump
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files. Thus this auxiliary information should be defined in the usual
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way, e.g. in a data file read in by a <A HREF = "read_data.html">read_data</A>
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command, before using the read_dump command, or by the <A HREF = "set.html">set</A>
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command, after the dump snapshot is read.
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</P>
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<HR>
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<P>If the dump filename specified as <I>file</I> ends with ".gz", the dump
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file is read in gzipped format. You cannot (yet) read a dump file
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that was written in binary format with a ".bin" suffix, or to multiple
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files via the "%" option in the dump file name. See the
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<A HREF = "dump.html">dump</A> command for details.
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</P>
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<P>The format of the dump file is selected through the <I>format</I> keyword.
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If specified, it must be the last keyword used, since all remaining
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arguments are passed on to the dump reader. The <I>native</I> format is
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for native LAMMPS dump files, written with a "dump atom".html or <A HREF = "dump.html">dump
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custom</A> command. The <I>xyz</I> format is for generic XYZ
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formatted dump files,
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</P>
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<P>The <I>molfile</I> format supports reading data through using the <A HREF = "vmd">VMD</A>
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molfile plugin interface. This dump reader format is only available,
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if the USER-MOLFILE package has been installed when compiling
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LAMMPS.
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</P>
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<P>The <I>molfile</I> format takes one or two additional values. The <I>style</I>
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value determines the file format to be used and can be any format that
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the molfile plugins support, such as DCD or XYZ. Note that DCD dump
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files can be written by LAMMPS via the <A HREF = "dump.html">dump dcd</A> command.
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The <I>path</I> value specifies a list of directories which LAMMPS will
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search for the molfile plugins appropriate to the specified <I>style</I>.
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The syntax of the <I>path</I> value is like other search paths: it can
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contain multiple directories separated by a colon (or semi-colon on
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windows). The <I>path</I> keyword is optional and defaults to ".",
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i.e. the current directory.
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</P>
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<P>Support for other dump format readers may be added in the future.
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</P>
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<HR>
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<P>Global information is first read from the dump file, namely timestep
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and box information.
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</P>
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<P>The dump file is scanned for a snapshot with a time stamp that matches
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the specified <I>Nstep</I>. This means the LAMMPS timestep the dump file
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snapshot was written on for the <I>native</I> format. However, the <I>xyz</I>
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and <I>molfile</I> formats do not store the timestep. For these formats,
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timesteps are numbered logically, in a sequential manner, starting
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from 0. Thus to access the 10th snapshot in an <I>xyz</I> or <I>mofile</I>
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formatted dump file, use <I>Nstep</I> = 9.
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</P>
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<P>The dimensions of the simulation box for the selected snapshot are
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also read; see the <I>box</I> keyword discussion below. For the <I>native</I>
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format, an error is generated if the snapshot is for a triclinic box
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and the current simulation box is orthogonal or vice versa. A warning
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will be generated if the snapshot box boundary conditions (periodic,
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shrink-wrapped, etc) do not match the current simulation boundary
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conditions, but the boundary condition information in the snapshot is
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otherwise ignored. See the "boundary" command for more details.
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</P>
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<P>For the <I>xyz</I> format, no information about the box is available, so
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you must set the <I>box</I> flag to <I>no</I>. See details below.
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</P>
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<P>For the <I>molfile</I> format, reading simulation box information is
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typically supported, but the location of the simulation box origin is
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lost and no explicit information about periodicity or
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orthogonal/triclinic box shape is available. The USER-MOLFILE package
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makes a best effort to guess based on heuristics, but this may not
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always work perfectly.
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</P>
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<HR>
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<P>Per-atom information from the dump file snapshot is then read from the
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dump file snapshot. This corresponds tot the specified <I>fields</I>
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listed in the read_dump command. It is an error to specify a
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z-dimension field, namely <I>z</I>, <I>vz</I>, or <I>iz</I>, for a 2d simulation.
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</P>
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<P>For dump files in <I>native</I> format, each column of per-atom data has a
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text label listed in the file. A matching label for each field must
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appear, e.g. the label "vy" for the field <I>vy</I>. For the <I>x</I>, <I>y</I>, <I>z</I>
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fields any of the following labels are considered a match:
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</P>
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<PRE>x, xs, xu, xsu for field <I>x</I>
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y, ys, yu, ysu for field <I>y</I>
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z, zs, zu, zsu for field <I>z</I>
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</PRE>
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<P>The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
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unwrapped) is explained on the <A HREF = "dump.html">dump</A> command doc page.
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These labels are searched for in the list of column labels in the dump
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file, in order, until a match is found.
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</P>
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<P>The dump file must also contain atom IDs, with a column label of "id".
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</P>
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<P>If the <I>add</I> keyword is specified with a value of <I>yes</I>, as discussed
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below, the dump file must contain atom types, with a column label of
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"type".
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</P>
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<P>If a column label in the dump file is not a match to a specified
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field, the <I>label</I> keyword can be used to specify which column label
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to associate with that field. An example is if a time-averaged
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coordinate is written to the dump file via the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command. The column will then have a
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label corresponding to the fix-ID rather than "x" or "xs". The
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<I>label</I> keyword can also be used to specify new column labels for
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fields <I>id</I> and <I>type</I>.
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</P>
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<P>For dump files in <I>xyz</I> format, only the <I>x</I>, <I>y</I>, and <I>z</I> fields are
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supported. The dump file does not store atom IDs, so these are
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assigned consecutively to the atoms as they appear in the dump file,
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starting from 1. Thus you should insure that order of atoms is
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consistent from snapshot to snapshot in the the XYZ dump file. See
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the <A HREF = "dump_modify.html">dump_modify sort</A> command if the XYZ dump file
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was written by LAMMPS.
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</P>
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<P>For dump files in <I>molfile</I> format, the <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, and
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<I>vz</I> fields can be specified. However, not all molfile formats store
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velocities, or their respective plugins may not support reading of
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velocities. The molfile dump files do not store atom IDs, so these
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are assigned consecutively to the atoms as they appear in the dump
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file, starting from 1. Thus you should insure that order of atoms are
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consistent from snapshot to snapshot in the the molfile dump file.
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See the <A HREF = "dump_modify.html">dump_modify sort</A> command if the dump file
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was written by LAMMPS.
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</P>
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<HR>
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<P>Information from the dump file snapshot is used to overwrite or
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replace properties of the current system. There are various options
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for how this is done, determined by the specified fields and optional
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keywords.
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</P>
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<P>The timestep of the snapshot becomes the current timestep for the
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simulation. See the <A HREF = "reset_timestep.html">reset_timestep</A> command if
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you wish to change this after the dump snapshot is read.
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</P>
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<P>If the <I>box</I> keyword is specified with a <I>yes</I> value, then the current
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simulation box dimensions are replaced by the dump snapshot box
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dimensions. If the <I>box</I> keyword is specified with a <I>no</I> value, the
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current simulatoin box is unchanged.
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</P>
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<P>If the <I>purge</I> keyword is specified with a <I>yes</I> value, then all
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current atoms in the system are deleted before any of the operations
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invoked by the <I>replace</I>, <I>trim</I>, or <I>add</I> keywords take place.
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</P>
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<P>If the <I>replace</I> keyword is specified with a <I>yes</I> value, then atoms
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with IDs that are in both the current system and the dump snapshot
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have their properties overwritten by field values. If the <I>replace</I>
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keyword is specified with a <I>no</I> value, atoms with IDs that are in
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both the current system and the dump snapshot are not modified.
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</P>
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<P>If the <I>trim</I> keyword is specified with a <I>yes</I> value, then atoms with
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IDs that are in the current system but not in the dump snapshot are
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deleted. These atoms are unaffected if the <I>trim</I> keyword is
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specified with a <I>no</I> value.
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</P>
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<P>If the <I>add</I> keyword is specified with a <I>yes</I> value, then atoms with
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IDs that are in the dump snapshot, but not in the current system are
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added to the system. These dump atoms are ignored if the <I>add</I>
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keyword is specified with a <I>no</I> value.
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</P>
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<P>Note that atoms added via the <I>add</I> keyword will have only the
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attributes read from the dump file due to the <I>field</I> arguments. If
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<I>x</I> or <I>y</I> or <I>z</I> is not specified as a field, a value of 0.0 is used
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for added atoms. Added atoms must have an atom type, so this value
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must appear in the dump file.
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</P>
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<P>Any other attributes (e.g. charge or particle diameter for spherical
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particles) will be set to default values, the same as if the
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<A HREF = "create_atoms.html">create_atoms</A> command were used.
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</P>
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<P>Note that atom IDs are not preserved for new dump snapshot atoms added
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via the <I>add</I> keyword. The procedure for assigning new atom IDS to
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added atoms is the same as is described for the
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<A HREF = "create_atoms.html">create_atoms</A> command.
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</P>
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<HR>
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<P>Atom coordinates read from the dump file are converted into absolute,
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unscaled coordinates, relative to the box dimensions of the snapshot.
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These coordinates may then be assigned to an existing or new atom in
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the current simulation. The coordinates will be remapped to the
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simulation box, whether it is the original box or the dump snapshot
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box. If periodic boundary conditiona apply, this means the atom will
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be remapped back into the box if necessary. If shrink-wrap boundary
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conditions apply, the new coordinates may change the current box
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dimensions. If fixed boundary conditions apply, the atom will be lost
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if it is outside the simulation box.
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</P>
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<P>For <I>native</I> format dump files, the 3 xyz image flags for an atom in
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the dump file are set to the corresponding values appearing in the
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dump file if the <I>ix</I>, <I>iy</I>, <I>iz</I> fields are specified. If not
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specified, the image flags for replaced atoms are not changed and
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image flags for new atoms are set to default values. The remapping
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procedure described in the previous paragraph can change images flags
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for all atoms (old and new) if periodic boundary conditions are
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applied to remap an atom back into the simulation box. Note that
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inconsistent image flag values can result if you use image flag fields
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from the dump file but do not also use the dump file box parameters.
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</P>
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<P>LAMMPS knows how to compute absolute, unscaled coordinates for the
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snapshot column labels discussed above, e.g. <I>x</I>, <I>xs</I>, <I>xu</I>, <I>xsu</I>.
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If another column label is assigned to the <I>x</I> or <I>y</I> or <I>z</I> field via
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the <I>label</I> keyword, e.g. for coordinates output by the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command, then LAMMPS needs to know whether
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the coordinate information in the dump file is scaled or unscaled.
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This can be set via the <I>scaled</I> keyword. The value of the <I>scaled</I>
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keyword is ignored for field <I>x</I> or <I>y</I> or <I>z</I> if the <I>label</I> keyword
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is not used to assign a column label to that field.
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</P>
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<P>The scaled vs unscaled setting must be consistent for any of the <I>x</I>,
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<I>y</I>, <I>z</I> fields that are specified. If the dump file coordinates are
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scaled and the simulation box is triclinic, then all 3 of the <I>x</I>,
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<I>y</I>, <I>z</I> fields must be specified, since they are all needed to
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generate absolute, unscaled coordinates.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>To read gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
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LAMMPS</A> section of the documentation.
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</P>
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<P>The <I>molfile</I> dump file formats are part of the USER-MOLFILE package.
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They are only enabled if LAMMPS was built with that packages. See the
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<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_molfile.html">dump molfile</A>,
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<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
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<A HREF = "rerun.html">rerun</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are box = yes, replace = yes, purge = no, trim =
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no, add = no, scaled = no, and format = native.
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</P>
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</HTML>
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