forked from lijiext/lammps
230 lines
10 KiB
Plaintext
230 lines
10 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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read_dump command :h3
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[Syntax:]
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read_dump file Nstep field1 field2 ... keyword values ... :pre
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file = name of dump file to read :ulb,l
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Nstep = snapshot timestep to read from file :l
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one or more fields may be appended :l
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field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {ix} or {iy} or {iz}
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{x},{y},{z} = atom coordinates
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{vx},{vy},{vz} = velocity components
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{ix},{iy},{iz} = image flags in each dimension :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {format} :l
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{box} value = {yes} or {no} = replace simulation box with dump box
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{replace} value = {yes} or {no} = overwrite atoms with dump atoms
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{purge} value = {yes} or {no} = delete all atoms before adding dump atoms
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{trim} value = {yes} or {no} = trim atoms not in dump snapshot
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{add} value = {yes} or {no} = add new dump atoms to system
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{label} value = field column
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field = one of the listed fields or {id} or {type}
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column = label on corresponding column in dump file
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{scaled} value = {yes} or {no} = coords in dump file are scaled/unscaled
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{format} value = {native} = format of dump file :pre
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:ule
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[Examples:]
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read_dump dump.file 5000 x y z
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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 :pre
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[Description:]
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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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"read_restart"_read_restart.html and "read_data"_read_data.html
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commands and the "restart2data"_Section_tools.html#restart tool for
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alternative methods to do this. Also see the "rerun"_rerun.html
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command for a means of reading multiple snapshots from a dump file.
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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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"create_box"_create_box.html, "read_data"_read_data.html, or
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"read_restart"_read_restart.html commands. The read_dump command can
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reset the simulation box dimensions, as explained below.
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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 "read_data"_read_data.html
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command, before using the read_dump command, or by the "set"_set.html
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command, after the dump snapshot is read.
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:line
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The dump file must be in native LAMMPS format, meaning it was written
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with a "dump atom".html or "dump custom"_dump.html command. Support
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for other dump file formats may be added in the future. These will be
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added as options to the {format} keyword.
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If the filename ends with ".gz", the dump file is read in gzipped
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format. You cannot (yet) read a dump file that was written in binary
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format with a ".bin" suffix, or to multiple files via the "%" option
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in the dump file name. See the "dump"_dump.html command for details.
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The dump file is scanned for a snapshot with a time stamp that matches
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the specified {Nstep}. The dimensions of the simulation box for that
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snapshot are also read; see the {box} keyword discussion below. An
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error is generated if the snapshot is for a triclinic box and the
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current simulation box is orthogonal or vice versa. A warning will be
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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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Per-atom information from the dump file snapshot is then read in,
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corresponding to the specified {fields} listed in the read_dump
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command. It is an error to specify a z-dimension field ({z}, {vz},
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{iz}) for a 2d simulation.
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For dump files in native LAMMPS format, each column of per-atom data
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has a text label which is listed in the file. A matching label for
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each field must appear, e.g. the label "vy" for the field {vy}. For
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the {x}, {y}, {z} fields any of the following labels are considered a
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match:
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x, xs, xu, xsu for field {x}
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y, ys, yu, ysu for field {y}
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z, zs, zu, zsu for field {z} :pre
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The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
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unwrapped) is explained on the "dump"_dump.html 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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The dump file must also contain atom IDs, with a column label of "id".
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If a column label in the dump file is not a match to a specified
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field, the {label} 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 "fix
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ave/atom"_fix_ave_atom.html 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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{label} keyword can also be used to specify new column labels for
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fields {id} and {type}. Information for atom types is needed from the
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dump file shapshot when the {add} keyword is used; see the discussion
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below.
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:line
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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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The timestep of the snapshot becomes the current timestep for the
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simulation. See the "reset_timestep"_reset_timestep.html command if
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you wish to change this after the dump snapshot is read.
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If the {box} keyword is specified with a {yes} 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 {box} keyword is specified with a {no} value, the
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current simulatoin box is unchanged.
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If the {purge} keyword is specified with a {yes} 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 {replace}, {trim}, or {add} keywords take place.
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If the {replace} keyword is specified with a {yes} 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 {replace}
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keyword is specified with a {no} 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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If the {trim} keyword is specified with a {yes} 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 {trim} keyword is
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specified with a {no} value.
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If the {add} keyword is specified with a {yes} 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 ignored if the {add} keyword is
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specified with a {no} value.
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Note that atoms added via the {add} keyword will have only the
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attributes read from the dump file due to the {field} arguments. If
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{x} or {y} or {z} 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 per-atom
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attribute must also appear in the dump file snapshot, with a column
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label of "type". Any other attributes (e.g. charge or particle
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diameter for spherical particles) will be set to default values, the
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same as if the "create_atoms"_create_atoms.html command were used.
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Note that atom IDs are not preserved for new dump snapshot atoms added
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via the {add} 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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"create_atoms"_create_atoms.html command.
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:line
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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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The 3 xyz image flags for an atom in the dump file are set to values
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in the dump file if the {ix}, {iy}, {iz} 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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LAMMPS knows how to compute absolute, unscaled coordinates for the
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snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}.
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If another column label is assigned to the {x} or {y} or {z} field via
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the {label} keyword, e.g. for coordinates output by the "fix
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ave/atom"_fix_ave_atom.html 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 {scaled} keyword. The value of the {scaled}
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keyword is ignored for field {x} or {y} or {z} if the {label} keyword
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is not used to assign a column label to that field.
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The scaled vs unscaled setting must be consistent for any of the {x},
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{y}, {z} 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 {x},
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{y}, {z} fields must be specified, since they are all needed to
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generate absolute, unscaled coordinates.
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:line
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[Restrictions:]
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To read gzipped dump files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the "Making
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LAMMPS"_Section_start.html#start_2 section of the documentation.
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[Related commands:]
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"dump"_dump.html, "read_data"_read_data.html,
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"read_restart"_read_restart.html, "rerun"_rerun.html
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[Default:]
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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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