forked from lijiext/lammps
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199 lines
9.0 KiB
HTML
<HTML>
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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>dump_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>dump_modify dump-ID keyword values ...
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</PRE>
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<UL><LI>dump-ID = ID of dump to modify
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<LI>one or more keyword/value pairs may be appended
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<LI>keyword = <I>append</I> or <I>every</I> or <I>flush</I> or <I>format</I> or <I>image</I> or <I>label</I> or <I>precision</I> or <I>region</I> or <I>scale</I> or <I>sort</I> or <I>thresh</I> or <I>unwrap</I>
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<PRE> <I>append</I> arg = <I>yes</I> or <I>no</I>
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<I>element</I> args = E1 E2 ... EN, where N = # of atom types
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E1,...,EN = element name, e.g. C or Fe or Ga
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<I>every</I> arg = N
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N = dump every this many timesteps
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<I>first</I> arg = <I>yes</I> or <I>no</I>
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<I>format</I> arg = C-style format string for one line of output
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<I>flush</I> arg = <I>yes</I> or <I>no</I>
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<I>image</I> arg = <I>yes</I> or <I>no</I>
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<I>label</I> arg = string
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string = character string (e.g. BONDS) to use in header of dump local file
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<I>precision</I> arg = power-of-10 value from 10 to 1000000
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<I>region</I> arg = region-ID or "none"
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<I>scale</I> arg = <I>yes</I> or <I>no</I>
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<I>sort</I> arg = <I>yes</I> or <I>no</I>
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<I>thresh</I> args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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operation = "<" or "<=" or ">" or ">=" or "==" or "!="
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value = numeric value to compare to
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these 3 args can be replaced by the word "none" to turn off thresholding
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<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
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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>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Modify the parameters of a previously defined dump command. Not all
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parameters are relevant to all dump styles.
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</P>
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<P>The <I>append</I> keyword applies to all dump styles except <I>cfg</I> and <I>xtc</I>
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and <I>dcd</I>. It also applies only to text output files, not to binary
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or gzipped files. If specified as <I>yes</I>, then dump snapshots are
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appended to the end of an existing dump file. If specified as <I>no</I>,
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then a new dump file will be created which will overwrite an existing
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file with the same name. This keyword can only take effect if the
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dump_modify command is used after the <A HREF = "dump.html">dump</A> command, but
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before the first command that causes dump snapshots to be output,
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e.g. a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">minimize</A> command. Once the
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dump file has been opened, this keyword has no further effect.
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</P>
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<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I> style. It
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associates element names (e.g. H, C, Fe) with LAMMPS atom types, so
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that the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
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visualization package can render atoms with the appropriate size and
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color. An element name is specified for each atom type (1 to Ntype)
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in the simulation. The same element name can be given to multiple
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atom types.
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</P>
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<P>The <I>every</I> keyword changes the dump frequency originally specified by
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the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump <I>dcd</I> style.
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</P>
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<P>The <I>first</I> keyword determines whether a dump snapshot is written on
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the very first timestep after the dump command is invoked. This will
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always occur if the current timestep is a multiple of N, the frequency
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specified in the <A HREF = "dump.html">dump</A> command, including timestep 0. But
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if this is not the case, a dump snapshot will only be written if the
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setting of this keyword is <I>yes</I>. If it is <I>no</I>, which is the
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default, then it will not be written.
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</P>
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<P>The <I>flush</I> keyword determines whether a flush operation in invoked
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after a dump snapshot is written to the dump file. A flush insures
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the output in that file is current (no buffering by the OS), even if
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LAMMPS halts before the simulation completes. Flushes cannot be
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performed with dump style <I>xtc</I>.
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</P>
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<P>The text-based dump styles have a default C-style format string which
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simply specifies %d for integers and %g for real values. The <I>format</I>
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keyword can be used to override the default with a new C-style format
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string. Do not include a trailing "\n" newline character in the
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format string. This option has no effect on the <I>dcd</I> and <I>xtc</I> dump
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styles since they write binary files. Note that for the <I>cfg</I> style,
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the first two fields (atom id and type) are not actually written into
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the CFG file, though you must include formats for them in the format
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string.
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</P>
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<P>The <I>image</I> keyword applies only to the dump <I>atom</I> style. If the
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image value is <I>yes</I>, 3 flags are appended to each atom's coords which
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are the absolute box image of the atom in each dimension. For
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example, an x image flag of -2 with a normalized coord of 0.5 means
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the atom is in the center of the box, but has passed thru the box
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boundary 2 times and is really 2 box lengths to the left of its
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current coordinate. Note that for dump style <I>custom</I> these various
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values can be printed in the dump file by using the appropriate atom
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attributes in the dump command itself.
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</P>
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<P>The <I>label</I> keyword applies only to the dump <I>local</I> style. When
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it writes local informatoin, such as bond or angle topology
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to a dump file, it will use the specified <I>label</I> to format
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the header. By default this includes 2 lines:
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</P>
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<PRE>ITEM: NUMBER OF ENTRIES
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ITEM: ENTRIES ...
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</PRE>
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<P>The word "ENTRIES" will be replaced with the string specified,
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e.g. BONDS or ANGLES.
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</P>
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<P>The <I>precision</I> keyword only applies to the dump <I>xtc</I> style. A
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specified value of N means that coordinates are stored to 1/N
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nanometer accuracy, e.g. for N = 1000, the coordinates are written to
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1/1000 nanometer accuracy.
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</P>
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<P>The <I>region</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
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styles. If specified, only atoms in the region will be written to the
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dump file. Only one region can be applied as a filter (the last one
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specified). See the <A HREF = "region.html">region</A> command for more details.
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Note that a region can be defined as the "inside" or "outside" of a
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geometric shape, and it can be the "union" or "intersection" of a
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series of simpler regions.
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</P>
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<P>The <I>scale</I> keyword applies only to the dump <I>atom</I> style. A scale
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value of <I>yes</I> means atom coords are written in normalized units from
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0.0 to 1.0 in each box dimension. If the simluation box is triclinic
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(tilted), then all atom coords will still be between 0.0 and 1.0. A
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value of <I>no</I> means they are written in absolute distance units
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(e.g. Angstroms or sigma).
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</P>
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<P>The <I>sort</I> keyword applies only to the dump <I>cfg</I> style. A sort value
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of <I>yes</I> means atoms will be written into the CFG file in sorted
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order, sorted by the atom ID. A value of <I>no</I> means a sort will not
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be performed and that atoms may be in an indeterminate order,
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depending on which processor owns which atoms.
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</P>
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<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I>
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styles. Multiple thresholds can be specified. Specifying "none"
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turns off all threshold criteria. If thresholds are specified, only
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atoms whose attributes meet all the threshold criteria are written to
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the dump file. The possible attributes that can be tested for are the
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same as those that can be specified in the <A HREF = "dump.html">dump custom</A>
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command. Note that different attributes can be output by the dump
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custom command than are used as threshold criteria by the dump_modify
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command. E.g. you can output the coordinates and stress of atoms
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whose energy is above some threshold.
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</P>
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<P>The <I>unwrap</I> keyword only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
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If set to <I>yes</I>, coordinates will be written "unwrapped" by the image
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flags for each atom. Unwrapped means that if the atom has passed thru
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a periodic boundary one or more times, the value is printed for what
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the coordinate would be if it had not been wrapped back into the
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periodic box. Note that these coordinates may thus be far outside the
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box size stored with the snapshot.
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</P>
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<P><B>Restrictions:</B> none
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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 = "undump.html">undump</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
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</P>
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<UL><LI>append = no
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<LI>element = "C" for every atom type
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<LI>every = whatever it was set to via the <A HREF = "dump.html">dump</A> command
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<LI>first = no
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<LI>flush = yes (except for the dump <I>xtc</I> style)
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<LI>format = %d and %g for each integer or floating point value
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<LI>image = no
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<LI>label = ENTRIES
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<LI>precision = 1000
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<LI>region = none
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<LI>scale = yes
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<LI>sort = no
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<LI>thresh = none
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<LI>unwrap = no
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</UL>
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</HTML>
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