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640 lines
34 KiB
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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>acolor</I> or <I>adiam</I> or <I>amap</I> or <I>append</I> or <I>bcolor</I> or <I>bdiam</I> or <I>backcolor</I> or <I>boxcolor</I> or <I>color</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>acolor</I> args = type color
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type = atom type or range of types (see below)
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color = name of color or color1/color2/...
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<I>adiam</I> args = type diam
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type = atom type or range of types (see below)
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diam = diameter of atoms of that type (distance units)
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<I>amap</I> args = lo hi style delta N entry1 entry2 ... entryN
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lo = number or <I>min</I> = lower bound of range of color map
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hi = number or <I>max</I> = upper bound of range of color map
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style = 2 letters = "c" or "d" or "s" plus "a" or "f"
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"c" for continuous
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"d" for discrete
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"s" for sequential
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"a" for absolute
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"f" for fractional
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delta = binsize (only used for style "s", otherwise ignored)
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binsize = range is divided into bins of this width
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N = # of subsequent entries
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entry = value color (for continuous style)
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value = number or <I>min</I> or <I>max</I> = single value within range
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color = name of color used for that value
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entry = lo hi color (for discrete style)
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lo/hi = number or <I>min</I> or <I>max</I> = lower/upper bound of subset of range
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color = name of color used for that subset of values
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entry = color (for sequential style)
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color = name of color used for a bin of values
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<I>append</I> arg = <I>yes</I> or <I>no</I>
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<I>bcolor</I> args = type color
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type = bond type or range of types (see below)
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color = name of color or color1/color2/...
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<I>bdiam</I> args = type diam
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type = bond type or range of types (see below)
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diam = diameter of bonds of that type (distance units)
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<I>backcolor</I> arg = color
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color = name of color for background
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<I>boxcolor</I> arg = color
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color = name of color for box lines
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<I>color</I> args = name R G B
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name = name of color
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R,G,B = red/green/blue numeric values from 0.0 to 1.0
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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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N can be a variable (see below)
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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>pad</I> arg = Nchar = # of characters to convert timestep to
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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>off</I> or <I>id</I> or N or -N
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off = no sorting of per-atom lines within a snapshot
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id = sort per-atom lines by atom ID
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N = sort per-atom lines in ascending order by the Nth column
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-N = sort per-atom lines in descending order by the Nth column
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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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dump_modify 1 every 1000
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dump_modify 1 every v_myVar
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dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
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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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<HR>
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<P>The <I>acolor</I> keyword applies only to the dump <I>image</I> style. It can
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be used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
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color setting is <I>type</I>, to set the color that atoms of each type will
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be drawn in the image.
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</P>
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<P>The specified <I>type</I> should be an integer from 1 to Ntypes = the
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number of atom types. A wildcard asterisk can be used in place of or
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in conjunction with the <I>type</I> argument to specify a range of atom
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types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
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number of atom types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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</P>
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<P>The specified <I>color</I> can be a single color which is any of the 140
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pre-defined colors (see below) or a color name defined by the
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dump_modify color option. Or it can be two or more colors separated
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by a "/" character, e.g. red/green/blue. In the former case, that
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color is assigned to all the specified atom types. In the latter
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case, the list of colors are assigned in a round-robin fashion to each
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of the specified atom types.
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</P>
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<HR>
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<P>The <I>adiam</I> keyword applies only to the dump <I>image</I> style. It can be
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used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
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diameter setting is <I>type</I>, to set the size that atoms of each type
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will be drawn in the image. The specified <I>type</I> should be an integer
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from 1 to Ntypes. As with the <I>acolor</I> keyword, a wildcard asterisk
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can be used as part of the <I>type</I> argument to specify a range of atomt
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types. The specified <I>diam</I> is the size in whatever distance
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<A HREF = "units.html">units</A> the input script is using, e.g. Angstroms.
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</P>
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<HR>
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<P>The <I>amap</I> keyword applies only to the dump <I>image</I> style. It can be
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used with the <A HREF = "dump_image.html">dump image</A> command, with its <I>atom</I>
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keyword, when its atom setting is an atom-attribute, to setup a color
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map. The color map is used to assign a specific RGB (red/green/blue)
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color value to an individual atom when it is drawn, based on the
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atom's attribute, which is a numeric value, e.g. its x-component of
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velocity if the atom-attribute "vx" was specified.
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</P>
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<P>The basic idea of a color map is that the atom-attribute will be
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within a range of values, and that range is associated with a a series
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of colors (e.g. red, blue, green). An atom's specific value (vx =
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-3.2) can then mapped to the series of colors (e.g. halfway between
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red and blue), and a specific color is determined via an interpolation
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procedure.
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</P>
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<P>There are many possible options for the color map, enabled by the
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<I>amap</I> keyword. Here are the details.
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</P>
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<P>The <I>lo</I> and <I>hi</I> settings determine the range of values allowed for
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the atom attribute. If numeric values are used for <I>lo</I> and/or <I>hi</I>,
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then values that are lower/higher than that value are set to the
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value. I.e. the range is static. If <I>lo</I> is specified as <I>min</I> or
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<I>hi</I> as <I>max</I> then the range is dynamic, and the lower and/or
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upper bound will be calculated each time an image is drawn, based
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on the set of atoms being visualized.
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</P>
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<P>The <I>style</I> setting is two letters, such as "ca". The first letter is
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either "c" for continuous, "d" for discrete, or "s" for sequential.
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The second letter is either "a" for absolute, or "f" for fractional.
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</P>
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<P>A continuous color map is one in which the color changes continuously
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from value to value within the range. A discrete color map is one in
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which discrete colors are assigned to sub-ranges of values within the
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range. A sequential color map is one in which discrete colors are
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assigned to a sequence of sub-ranges of values covering the entire
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range.
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</P>
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<P>An absolute color map is one in which the values to which colors are
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assigned are specified explicitly as values within the range. A
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fractional color map is one in which the values to which colors are
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assigned are specified as a fractional portion of the range. For
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example if the range is from -10.0 to 10.0, and the color red is to be
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assigned to atoms with a value of 5.0, then for an absolute color map
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the number 5.0 would be used. But for a fractional map, the number
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0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
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</P>
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<P>The <I>delta</I> setting must be specified for all styles, but is only used
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for the sequential style; otherwise the value is ignored. It
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specifies the bin size to use within the range for assigning
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consecutive colors to. For example, if the range is from -10.0 to
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10.0 and a <I>delta</I> of 1.0 is used, then 20 colors will be assigned to
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the range. The first will be from -10.0 <= color1 < -9.0, then 2nd
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from -9.0 <= color2 < -8.0, etc.
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</P>
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<P>The <I>N</I> setting is how many entries follow. The format of the entries
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depends on whether the color map style is continuous, discrete or
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sequential. In all cases the <I>color</I> setting can be any of the 140
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pre-defined colors (see below) or a color name defined by the
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dump_modify color option.
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</P>
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<P>For continuous color maps, each entry has a <I>value</I> and a <I>color</I>.
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The <I>value</I> is either a number within the range of values or <I>min</I> or
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<I>max</I>. The <I>value</I> of the first entry must be <I>min</I> and the <I>value</I>
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of the last entry must be <I>max</I>. Any entries in between must have
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increasing values. Note that numeric values can be specified either
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as absolute numbers or as fractions (0.0 to 1.0) of the range,
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depending on the "a" or "f" in the style setting for the color map.
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</P>
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<P>Here is how the entries are used to determine the color of an
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individual atom, given the value X of its atom attribute. X will fall
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between 2 of the entry values. The color of the atom is linearly
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interpolated (in each of the RGB values) between the 2 colors
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associated with those entries. For example, if X = -5.0 and the 2
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surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
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atom's color will be halfway between "red" and "blue", which happens
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to be "purple".
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</P>
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<P>For discrete color maps, each entry has a <I>lo</I> and <I>hi</I> value and a
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<I>color</I>. The <I>lo</I> and <I>hi</I> settings are either numbers within the
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range of values or <I>lo</I> can be <I>min</I> or <I>hi</I> can be <I>max</I>. The <I>lo</I>
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and <I>hi</I> settings of the last entry must be <I>min</I> and <I>max</I>. Other
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entries can have any <I>lo</I> and <I>hi</I> values and the sub-ranges of
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different values can overlap. Note that numeric <I>lo</I> and <I>hi</I> values
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can be specified either as absolute numbers or as fractions (0.0 to
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1.0) of the range, depending on the "a" or "f" in the style setting
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for the color map.
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</P>
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<P>Here is how the entries are used to determine the color of an
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individual atom, given the value X of its atom attribute. The entries
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are scanned from first to last. The first time that <I>lo</I> <= X <=
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<I>hi</I>, X is assigned the color associated with that entry. You can
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think of the last entry as assigning a default color (since it will
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always be matched by X), and the earlier entries as colors that
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override the default. Also note that no interpolation of a color RGB
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is done. All atoms will be drawn with one of the colors in the list
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of entries.
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</P>
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<P>For sequential color maps, each entry has only a <I>color</I>. Here is how
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the entries are used to determine the color of an individual atom,
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given the value X of its atom attribute. The range is partitioned
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into N bins of width <I>binsize</I>. Thus X will fall in a specific bin
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from 1 to N, say the Mth bin. If it falls on a boundary between 2
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bins, it is considered to be in the higher of the 2 bins. Each bin is
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assigned a color from the E entries. If E < N, then the colors are
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repeated. For example if 2 entries with colors red and green are
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specified, then the odd numbered bins will be red and the even bins
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green. The color of the atom is the color of its bin. Note that the
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sequential color map is really a shorthand way of defining a discrete
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color map without having to specify where all the bin boundaries are.
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</P>
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<HR>
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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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<HR>
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<P>The <I>bcolor</I> keyword applies only to the dump <I>image</I> style. It can
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be used with the <A HREF = "dump_image.html">dump image</A> command, with its <I>bond</I>
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keyword, when its color setting is <I>type</I>, to set the color that bonds
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of each type will be drawn in the image.
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</P>
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<P>The specified <I>type</I> should be an integer from 1 to Nbondtypes = the
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number of bond types. A wildcard asterisk can be used in place of or
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in conjunction with the <I>type</I> argument to specify a range of bond
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types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
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number of bond types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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</P>
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<P>The specified <I>color</I> can be a single color which is any of the 140
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pre-defined colors (see below) or a color name defined by the
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dump_modify color option. Or it can be two or more colors separated
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by a "/" character, e.g. red/green/blue. In the former case, that
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color is assigned to all the specified bond types. In the latter
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case, the list of colors are assigned in a round-robin fashion to each
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of the specified bond types.
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</P>
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<HR>
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<P>The <I>bdiam</I> keyword applies only to the dump <I>image</I> style. It can be
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used with the <A HREF = "dump_image.html">dump image</A> command, with its <I>bond</I>
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keyword, when its diam setting is <I>type</I>, to set the diameter that
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bonds of each type will be drawn in the image. The specified <I>type</I>
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should be an integer from 1 to Nbondtypes. As with the <I>bcolor</I>
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keyword, a wildcard asterisk can be used as part of the <I>type</I>
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argument to specify a range of bond types. The specified <I>diam</I> is
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the size in whatever distance <A HREF = "units.html">units</A> you are using,
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e.g. Angstroms.
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</P>
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<HR>
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<P>The <I>backcolor</I> keyword applies only to the dump <I>image</I> style. It
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sets the background color of the images. The color name can be any of
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the 140 pre-defined colors (see below) or a color name defined by the
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dump_modify color option.
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</P>
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<HR>
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<P>The <I>boxcolor</I> keyword applies only to the dump <I>image</I> style. It
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sets the color of the simulation box drawn around the atoms in each
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image. See the "dump image box" command for how to specify that a box
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be drawn. The color name can be any of the 140 pre-defined colors
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(see below) or a color name defined by the dump_modify color option.
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</P>
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<HR>
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<P>The <I>color</I> keyword applies only to the dump <I>image</I> style. It allows
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definition of a new color name, in addition to the 140-predefined
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colors (see below), and associates 3 red/green/blue RGB values with
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that color name. The color name can then be used with any other
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dump_modify keyword that takes a color name as a value. The RGB
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values should each be floating point values between 0.0 and 1.0
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inclusive.
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</P>
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<P>When a color name is converted to RGB values, the user-defined color
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names are searched first, then the 140 pre-defined color names. This
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means you can also use the <I>color</I> keyword to overwrite one of the
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pre-defined color names with new RBG values.
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</P>
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<HR>
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<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I>, <I>xyz</I>, and
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<I>image</I> styles. It associates element names (e.g. H, C, Fe) with
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LAMMPS atom types. See the list of element names at the bottom of
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this page.
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</P>
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<P>In the case of dump <I>cfg</I>, this allows the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
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visualization package to read the dump file and render atoms with the
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appropriate size and color.
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</P>
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<P>In the case of dump <I>image</I>, the output images will follow the same
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<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> convention. An element name is specified for each
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atom type (1 to Ntype) in the simulation. The same element name can
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be given to multiple atom types.
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</P>
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<P>In the case of <I>xyz</I> format dumps, there are no restrictions to what
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label can be used as an element name. Any whitespace separated text
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will be accepted.
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</P>
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<HR>
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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. The every keyword can be
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specified in one of two ways. It can be a numeric value in which case
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it must be > 0. Or it can be an <A HREF = "variable.html">equal-style variable</A>,
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which should be specified as v_name, where name is the variable name.
|
|
</P>
|
|
<P>In this case, the variable is evaluated at the beginning of a run to
|
|
determine the next timestep at which a dump snapshot will be written
|
|
out. On that timestep the variable will be evaluated again to
|
|
determine the next timestep, etc. Thus the variable should return
|
|
timestep values. See the stagger() and logfreq() and stride() math
|
|
functions for <A HREF = "variable.html">equal-style variables</A>, as examples of
|
|
useful functions to use in this context. Other similar math functions
|
|
could easily be added as options for <A HREF = "variable.html">equal-style
|
|
variables</A>. Also see the next() function, which allows
|
|
use of a file-style variable which reads successive values from a
|
|
file, each time the variable is evaluated. Used with the <I>every</I>
|
|
keyword, if the file contains a list of ascending timesteps, you can
|
|
output snapshots whenever you wish.
|
|
</P>
|
|
<P>Note that when using the variable option with the <I>every</I> keyword, you
|
|
need to use the <I>first</I> option if you want an initial snapshot written
|
|
to the dump file. The <I>every</I> keyword cannot be used with the dump
|
|
<I>dcd</I> style.
|
|
</P>
|
|
<P>For example, the following commands will
|
|
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
|
|
</P>
|
|
<PRE>variable s equal logfreq(10,3,10)
|
|
dump 1 all atom 100 tmp.dump
|
|
dump_modify 1 every v_s first yes
|
|
</PRE>
|
|
<P>The following commands would write snapshots at the timesteps listed
|
|
in file tmp.times:
|
|
</P>
|
|
<PRE>variable f file tmp.times
|
|
variable s equal next(f)
|
|
dump 1 all atom 100 tmp.dump
|
|
dump_modify 1 every v_s
|
|
</PRE>
|
|
<P>IMPORTANT NOTE: When using a file-style variable with the <I>every</I>
|
|
keyword, the file of timesteps must list a first timestep that is
|
|
beyond the current timestep (e.g. it cannot be 0). And it must list
|
|
one or more timesteps beyond the length of the run you perform. This
|
|
is because the dump command will generate an error if the next
|
|
timestep it reads from the file is not a value greater than the
|
|
current timestep. Thus if you wanted output on steps 0,15,100 of a
|
|
100-timestep run, the file should contain the values 15,100,101 and
|
|
you should also use the dump_modify first command. Any final value >
|
|
100 could be used in place of 101.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>first</I> keyword determines whether a dump snapshot is written on
|
|
the very first timestep after the dump command is invoked. This will
|
|
always occur if the current timestep is a multiple of N, the frequency
|
|
specified in the <A HREF = "dump.html">dump</A> command, including timestep 0. But
|
|
if this is not the case, a dump snapshot will only be written if the
|
|
setting of this keyword is <I>yes</I>. If it is <I>no</I>, which is the
|
|
default, then it will not be written.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>flush</I> keyword determines whether a flush operation is invoked
|
|
after a dump snapshot is written to the dump file. A flush insures
|
|
the output in that file is current (no buffering by the OS), even if
|
|
LAMMPS halts before the simulation completes. Flushes cannot be
|
|
performed with dump style <I>xtc</I>.
|
|
</P>
|
|
<P>The text-based dump styles have a default C-style format string which
|
|
simply specifies %d for integers and %g for real values. The <I>format</I>
|
|
keyword can be used to override the default with a new C-style format
|
|
string. Do not include a trailing "\n" newline character in the
|
|
format string. This option has no effect on the <I>dcd</I> and <I>xtc</I> dump
|
|
styles since they write binary files. Note that for the <I>cfg</I> style,
|
|
the first two fields (atom id and type) are not actually written into
|
|
the CFG file, though you must include formats for them in the format
|
|
string.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>image</I> keyword applies only to the dump <I>atom</I> style. If the
|
|
image value is <I>yes</I>, 3 flags are appended to each atom's coords which
|
|
are the absolute box image of the atom in each dimension. For
|
|
example, an x image flag of -2 with a normalized coord of 0.5 means
|
|
the atom is in the center of the box, but has passed thru the box
|
|
boundary 2 times and is really 2 box lengths to the left of its
|
|
current coordinate. Note that for dump style <I>custom</I> these various
|
|
values can be printed in the dump file by using the appropriate atom
|
|
attributes in the dump command itself.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>label</I> keyword applies only to the dump <I>local</I> style. When
|
|
it writes local informatoin, such as bond or angle topology
|
|
to a dump file, it will use the specified <I>label</I> to format
|
|
the header. By default this includes 2 lines:
|
|
</P>
|
|
<PRE>ITEM: NUMBER OF ENTRIES
|
|
ITEM: ENTRIES ...
|
|
</PRE>
|
|
<P>The word "ENTRIES" will be replaced with the string specified,
|
|
e.g. BONDS or ANGLES.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>pad</I> keyword only applies when the dump filename is specified
|
|
with a wildcard "*" character which becomes the timestep. If <I>pad</I> is
|
|
0, which is the default, the timestep is converted into a string of
|
|
unpadded length, e.g. 100 or 12000 or 2000000. When <I>pad</I> is
|
|
specified with <I>Nchar</I> > 0, the string is padded with leading zeroes
|
|
so they are all the same length = <I>Nchar</I>. For example, pad 7 would
|
|
yield 0000100, 0012000, 2000000. This can be useful so that
|
|
post-processing programs can easily read the files in ascending
|
|
timestep order.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>precision</I> keyword only applies to the dump <I>xtc</I> style. A
|
|
specified value of N means that coordinates are stored to 1/N
|
|
nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
|
1/1000 nanometer accuracy.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>region</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I> and
|
|
<I>image</I> styles. If specified, only atoms in the region will be
|
|
written to the dump file or included in the image. Only one region
|
|
can be applied as a filter (the last one specified). See the
|
|
<A HREF = "region.html">region</A> command for more details. Note that a region can
|
|
be defined as the "inside" or "outside" of a geometric shape, and it
|
|
can be the "union" or "intersection" of a series of simpler regions.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>scale</I> keyword applies only to the dump <I>atom</I> style. A scale
|
|
value of <I>yes</I> means atom coords are written in normalized units from
|
|
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
|
|
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
|
value of <I>no</I> means they are written in absolute distance units
|
|
(e.g. Angstroms or sigma).
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>sort</I> keyword determines whether lines of per-atom output in a
|
|
snapshot are sorted or not. A sort value of <I>off</I> means they will
|
|
typically be written in indeterminate order, either in serial or
|
|
parallel. This is the case even in serial if the <A HREF = "atom_modify.html">atom_modify
|
|
sort</A> option is turned on, which it is by default, to
|
|
improve performance. A sort value of <I>id</I> means sort the output by
|
|
atom ID. A sort value of N or -N means sort the output by the value
|
|
in the Nth column of per-atom info in either ascending or descending
|
|
order. The dump <I>local</I> style cannot be sorted by atom ID, since
|
|
there are typically multiple lines of output per atom. Some dump
|
|
styles, such as <I>dcd</I> and <I>xtc</I>, require sorting by atom ID to format
|
|
the output file correctly.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Unless it is required by the dump style, sorting dump
|
|
file output requires extra overhead in terms of CPU and communication
|
|
cost, as well as memory, versus unsorted output.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> and <I>cfg</I> and
|
|
<I>image</I> styles. Multiple thresholds can be specified. Specifying
|
|
"none" turns off all threshold criteria. If thresholds are specified,
|
|
only atoms whose attributes meet all the threshold criteria are
|
|
written to the dump file or included in the image. The possible
|
|
attributes that can be tested for are the same as those that can be
|
|
specified in the <A HREF = "dump.html">dump custom</A> command, with the exception
|
|
of the <I>element</I> attribute, since it is not a numeric value. Note
|
|
that different attributes can be output by the dump custom command
|
|
than are used as threshold criteria by the dump_modify command.
|
|
E.g. you can output the coordinates and stress of atoms whose energy
|
|
is above some threshold.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>unwrap</I> keyword only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
|
|
If set to <I>yes</I>, coordinates will 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.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B> none
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>, <A HREF = "undump.html">undump</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are
|
|
</P>
|
|
<UL><LI>acolor = * red/green/blue/yellow/aqua/cyan
|
|
<LI>adiam = * 1.0
|
|
<LI>amap = min max cf 2 min blue max red
|
|
<LI>append = no
|
|
<LI>bcolor = * red/green/blue/yellow/aqua/cyan
|
|
<LI>bdiam = * 0.5
|
|
<LI>backcolor = black
|
|
<LI>boxcolor = yellow
|
|
<LI>color = 140 color names are pre-defined as listed below
|
|
<LI>element = "C" for every atom type
|
|
<LI>every = whatever it was set to via the <A HREF = "dump.html">dump</A> command
|
|
<LI>first = no
|
|
<LI>flush = yes
|
|
<LI>format = %d and %g for each integer or floating point value
|
|
<LI>image = no
|
|
<LI>label = ENTRIES
|
|
<LI>pad = 0
|
|
<LI>precision = 1000
|
|
<LI>region = none
|
|
<LI>scale = yes
|
|
<LI>sort = off for dump styles <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I>
|
|
<LI>sort = id for dump styles <I>dcd</I>, <I>xtc</I>, and <I>xyz</I>
|
|
<LI>thresh = none
|
|
<LI>unwrap = no
|
|
</UL>
|
|
<HR>
|
|
|
|
<P>These are the standard 109 element names that LAMMPS pre-defines for
|
|
use with the <A HREF = "dump_image.html">dump image</A> and dump_modify commands.
|
|
</P>
|
|
<UL><LI>1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
|
|
<LI>11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
|
|
<LI>21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
|
|
<LI>31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
|
|
<LI>41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
|
|
<LI>51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
|
|
<LI>61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
|
|
<LI>71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
|
|
<LI>81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
|
|
<LI>91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
|
|
<LI>101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
|
|
</UL>
|
|
<HR>
|
|
|
|
<P>These are the 140 colors that LAMMPS pre-defines for use with the
|
|
<A HREF = "dump_image.html">dump image</A> and dump_modify commands. Additional
|
|
colors can be defined with the dump_modify color command. The 3
|
|
numbers listed for each name are the RGB (red/green/blue) values.
|
|
Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >aliceblue = 240, 248, 255 </TD><TD >antiquewhite = 250, 235, 215 </TD><TD >aqua = 0, 255, 255 </TD><TD >aquamarine = 127, 255, 212 </TD><TD >azure = 240, 255, 255 </TD></TR>
|
|
<TR><TD >beige = 245, 245, 220 </TD><TD >bisque = 255, 228, 196 </TD><TD >black = 0, 0, 0 </TD><TD >blanchedalmond = 255, 255, 205 </TD><TD >blue = 0, 0, 255 </TD></TR>
|
|
<TR><TD >blueviolet = 138, 43, 226 </TD><TD >brown = 165, 42, 42 </TD><TD >burlywood = 222, 184, 135 </TD><TD >cadetblue = 95, 158, 160 </TD><TD >chartreuse = 127, 255, 0 </TD></TR>
|
|
<TR><TD >chocolate = 210, 105, 30 </TD><TD >coral = 255, 127, 80 </TD><TD >cornflowerblue = 100, 149, 237 </TD><TD >cornsilk = 255, 248, 220 </TD><TD >crimson = 220, 20, 60 </TD></TR>
|
|
<TR><TD >cyan = 0, 255, 255 </TD><TD >darkblue = 0, 0, 139 </TD><TD >darkcyan = 0, 139, 139 </TD><TD >darkgoldenrod = 184, 134, 11 </TD><TD >darkgray = 169, 169, 169 </TD></TR>
|
|
<TR><TD >darkgreen = 0, 100, 0 </TD><TD >darkkhaki = 189, 183, 107 </TD><TD >darkmagenta = 139, 0, 139 </TD><TD >darkolivegreen = 85, 107, 47 </TD><TD >darkorange = 255, 140, 0 </TD></TR>
|
|
<TR><TD >darkorchid = 153, 50, 204 </TD><TD >darkred = 139, 0, 0 </TD><TD >darksalmon = 233, 150, 122 </TD><TD >darkseagreen = 143, 188, 143 </TD><TD >darkslateblue = 72, 61, 139 </TD></TR>
|
|
<TR><TD >darkslategray = 47, 79, 79 </TD><TD >darkturquoise = 0, 206, 209 </TD><TD >darkviolet = 148, 0, 211 </TD><TD >deeppink = 255, 20, 147 </TD><TD >deepskyblue = 0, 191, 255 </TD></TR>
|
|
<TR><TD >dimgray = 105, 105, 105 </TD><TD >dodgerblue = 30, 144, 255 </TD><TD >firebrick = 178, 34, 34 </TD><TD >floralwhite = 255, 250, 240 </TD><TD >forestgreen = 34, 139, 34 </TD></TR>
|
|
<TR><TD >fuchsia = 255, 0, 255 </TD><TD >gainsboro = 220, 220, 220 </TD><TD >ghostwhite = 248, 248, 255 </TD><TD >gold = 255, 215, 0 </TD><TD >goldenrod = 218, 165, 32 </TD></TR>
|
|
<TR><TD >gray = 128, 128, 128 </TD><TD >green = 0, 128, 0 </TD><TD >greenyellow = 173, 255, 47 </TD><TD >honeydew = 240, 255, 240 </TD><TD >hotpink = 255, 105, 180 </TD></TR>
|
|
<TR><TD >indianred = 205, 92, 92 </TD><TD >indigo = 75, 0, 130 </TD><TD >ivory = 255, 240, 240 </TD><TD >khaki = 240, 230, 140 </TD><TD >lavender = 230, 230, 250 </TD></TR>
|
|
<TR><TD >lavenderblush = 255, 240, 245 </TD><TD >lawngreen = 124, 252, 0 </TD><TD >lemonchiffon = 255, 250, 205 </TD><TD >lightblue = 173, 216, 230 </TD><TD >lightcoral = 240, 128, 128 </TD></TR>
|
|
<TR><TD >lightcyan = 224, 255, 255 </TD><TD >lightgoldenrodyellow = 250, 250, 210 </TD><TD >lightgreen = 144, 238, 144 </TD><TD >lightgrey = 211, 211, 211 </TD><TD >lightpink = 255, 182, 193 </TD></TR>
|
|
<TR><TD >lightsalmon = 255, 160, 122 </TD><TD >lightseagreen = 32, 178, 170 </TD><TD >lightskyblue = 135, 206, 250 </TD><TD >lightslategray = 119, 136, 153 </TD><TD >lightsteelblue = 176, 196, 222 </TD></TR>
|
|
<TR><TD >lightyellow = 255, 255, 224 </TD><TD >lime = 0, 255, 0 </TD><TD >limegreen = 50, 205, 50 </TD><TD >linen = 250, 240, 230 </TD><TD >magenta = 255, 0, 255 </TD></TR>
|
|
<TR><TD >maroon = 128, 0, 0 </TD><TD >mediumaquamarine = 102, 205, 170 </TD><TD >mediumblue = 0, 0, 205 </TD><TD >mediumorchid = 186, 85, 211 </TD><TD >mediumpurple = 147, 112, 219 </TD></TR>
|
|
<TR><TD >mediumseagreen = 60, 179, 113 </TD><TD >mediumslateblue = 123, 104, 238 </TD><TD >mediumspringgreen = 0, 250, 154 </TD><TD >mediumturquoise = 72, 209, 204 </TD><TD >mediumvioletred = 199, 21, 133 </TD></TR>
|
|
<TR><TD >midnightblue = 25, 25, 112 </TD><TD >mintcream = 245, 255, 250 </TD><TD >mistyrose = 255, 228, 225 </TD><TD >moccasin = 255, 228, 181 </TD><TD >navajowhite = 255, 222, 173 </TD></TR>
|
|
<TR><TD >navy = 0, 0, 128 </TD><TD >oldlace = 253, 245, 230 </TD><TD >olive = 128, 128, 0 </TD><TD >olivedrab = 107, 142, 35 </TD><TD >orange = 255, 165, 0 </TD></TR>
|
|
<TR><TD >orangered = 255, 69, 0 </TD><TD >orchid = 218, 112, 214 </TD><TD >palegoldenrod = 238, 232, 170 </TD><TD >palegreen = 152, 251, 152 </TD><TD >paleturquoise = 175, 238, 238 </TD></TR>
|
|
<TR><TD >palevioletred = 219, 112, 147 </TD><TD >papayawhip = 255, 239, 213 </TD><TD >peachpuff = 255, 239, 213 </TD><TD >peru = 205, 133, 63 </TD><TD >pink = 255, 192, 203 </TD></TR>
|
|
<TR><TD >plum = 221, 160, 221 </TD><TD >powderblue = 176, 224, 230 </TD><TD >purple = 128, 0, 128 </TD><TD >red = 255, 0, 0 </TD><TD >rosybrown = 188, 143, 143 </TD></TR>
|
|
<TR><TD >royalblue = 65, 105, 225 </TD><TD >saddlebrown = 139, 69, 19 </TD><TD >salmon = 250, 128, 114 </TD><TD >sandybrown = 244, 164, 96 </TD><TD >seagreen = 46, 139, 87 </TD></TR>
|
|
<TR><TD >seashell = 255, 245, 238 </TD><TD >sienna = 160, 82, 45 </TD><TD >silver = 192, 192, 192 </TD><TD >skyblue = 135, 206, 235 </TD><TD >slateblue = 106, 90, 205 </TD></TR>
|
|
<TR><TD >slategray = 112, 128, 144 </TD><TD >snow = 255, 250, 250 </TD><TD >springgreen = 0, 255, 127 </TD><TD >steelblue = 70, 130, 180 </TD><TD >tan = 210, 180, 140 </TD></TR>
|
|
<TR><TD >teal = 0, 128, 128 </TD><TD >thistle = 216, 191, 216 </TD><TD >tomato = 253, 99, 71 </TD><TD >turquoise = 64, 224, 208 </TD><TD >violet = 238, 130, 238 </TD></TR>
|
|
<TR><TD >wheat = 245, 222, 179 </TD><TD >white = 255, 255, 255 </TD><TD >whitesmoke = 245, 245, 245 </TD><TD >yellow = 255, 255, 0 </TD><TD >yellowgreen = 154, 205, 50
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
</HTML>
|