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456 lines
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>dump image 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 ID group-ID image N file color diameter keyword value ...
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</PRE>
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<UL><LI>ID = user-assigned name for the dump
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<LI>group-ID = ID of the group of atoms to be imaged
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<LI>image = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
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<LI>N = dump every this many timesteps
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<LI>file = name of file to write image to
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<LI>color = atom attribute that determines color of each atom
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<LI>diameter = atom attribute that determines size of each atom
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>adiam</I> or <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I>
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<PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
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<I>atom</I> = yes/no = do or do not draw atoms
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<I>bond</I> values = color width = color and width of bonds
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color = <I>atom</I> or <I>type</I> or <I>none</I>
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width = number or <I>atom</I> or <I>type</I> or <I>none</I>
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number = numeric value for bond width (distance units)
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<I>size</I> values = width height = size of images
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width = width of image in # of pixels
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height = height of image in # of pixels
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<I>view</I> values = theta phi = view of simulation box
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theta = view angle from +z axis (degrees)
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phi = azimuthal view angle (degrees)
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theta or phi can be a variable (see below)
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<I>center</I> values = flag Cx Cy Cz = center point of image
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flag = "s" for static, "d" for dynamic
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Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
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Cx,Cy,Cz can be variables (see below)
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<I>up</I> values = Ux Uy Uz = direction that is "up" in image
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Ux,Uy,Uz = components of up vector
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Ux,Uy,Uz can be variables (see below)
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<I>zoom</I> value = zfactor = size that simulation box appears in image
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zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
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zfactor can be a variable (see below)
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<I>persp</I> value = pfactor = amount of "perspective" in image
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pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
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pfactor can be a variable (see below)
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<I>box</I> values = yes/no diam = draw outline of simulation box
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yes/no = do or do not draw simulation box lines
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diam = diameter of box lines as fraction of shortest box length
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<I>axes</I> values = yes/no length diam = draw xyz axes
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yes/no = do or do not draw xyz axes lines next to simulation box
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length = length of axes lines as fraction of respective box lengths
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diam = diameter of axes lines as fraction of shortest box length
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<I>shiny</I> value = sfactor = shinyness of spheres and cylinders
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sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
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<I>ssao</I> value = yes/no seed dfactor = SSAO depth shading
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yes/no = turn depth shading on/off
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seed = random # seed (positive integer)
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dfactor = strength of shading from 0.0 to 1.0
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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 myDump all image 100 dump.*.jpg type type
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Dump a high-quality ray-traced image of the atom configuration every N
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timesteps as either a JPG or PPM file. A series of such images can
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easily be converted into an animated movie of your simulation; see
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further details below. Other dump styles store snapshots of numerical
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data asociated with atoms in various formats, as discussed on the
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<A HREF = "dump.html">dump</A> doc page.
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</P>
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<P>Here are two sample images, rendered as 1024x1024 JPG files. Click to
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see the full-size images:
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</P>
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<DIV ALIGN=center>
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<A HREF = "JPG/dump1.jpg"><IMG SRC = "JPG/dump1_small.jpg"></A>
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<A HREF = "JPG/dump2.jpg"><IMG SRC = "JPG/dump2_small.jpg"></A>
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</DIV>
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<P>Only atoms in the specified group are rendered in the image. The
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<A HREF = "dump_modify.html">dump_modify region and thresh</A> commands can also
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alter what atoms are included in the image.
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</P>
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<P>The filename suffix determines whether a JPG or PPM file is created.
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If the suffix is ".jpg" or ".jpeg", then a JPG file is created, else a
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PPM file is created, which is a text-based format. To write out JPG
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files, you must build LAMMPS with a JPEG library. See <A HREF = "Section_start.html#start_2_4">this
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section</A> of the manual for instructions
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on how to do this.
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</P>
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<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
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on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom in the image may be slightly outside the simulation box.
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</P>
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<HR>
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<P>Dumps are performed on timesteps that are a multiple of N (including
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timestep 0) and on the last timestep of a minimization if the
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minimization converges. Note that this means a dump will not be
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performed on the initial timestep after the dump command is invoked,
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if the current timestep is not a multiple of N. This behavior can be
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changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
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can be useful if the dump command is invoked after a minimization
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ended on an arbitrary timestep. N can be changed between runs by
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using the <A HREF = "dump_modify.html">dump_modify every</A> command.
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</P>
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<P>Dump image filenames must contain a wildcard character "*", so that
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one image file per snapshot is written. The "*" character is replaced
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with the timestep value. For example, tmp.dump.*.jpg becomes
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tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
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that the <A HREF = "dump_modify.html">dump_modify pad</A> command can be used to
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insure all timestep numbers are the same length (e.g. 00010), which
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can make it easier to convert a series of images into a movie in the
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correct ordering.
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</P>
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<HR>
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<P>The <I>color</I> and <I>diameter</I> settings determine the color and size of
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atoms rendered in the image. They can be any atom attribute defined
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for the <A HREF = "dump.html">dump custom</A> command, including <I>type</I> and
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<I>element</I>. This includes per-atom quantities calculated by a
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<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>,
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which are prefixed by "c_", "f_", or "v_" respectively. Note that the
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<I>diameter</I> setting can be overridden with a numeric value by the
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optional <I>adiam</I> keyword, in which case you can specify the <I>diameter</I>
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setting with any valid atom attribute.
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</P>
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<P>If <I>type</I> is specified for the <I>color</I> setting, then the color of each
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atom is determined by its atom type. By default the mapping of types
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to colors is as follows:
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</P>
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<UL><LI>type 1 = red
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<LI>type 2 = green
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<LI>type 3 = blue
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<LI>type 4 = yellow
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<LI>type 5 = aqua
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<LI>type 6 = cyan
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</UL>
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<P>and repeats itself for types > 6. This mapping can be changed by the
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<A HREF = "dump_modify.html">dump_modify acolor</A> command.
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</P>
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<P>If <I>type</I> is specified for the <I>diameter</I> setting then the diameter of
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each atom is determined by its atom type. By default all types have
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diameter 1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
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adiam</A> command.
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</P>
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<P>If <I>element</I> is specified for the <I>color</I> and/or <I>diameter</I> setting,
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then the color and/or diameter of each atom is determined by which
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element it is, which in turn is specified by the element-to-type
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mapping specified by the "dump_modify element" command. By default
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every atom type is C (carbon). Every element has a color and diameter
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associated with it, which is the same as the colors and sizes used by
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the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
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</P>
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<P>If other atom attributes are used for the <I>color</I> or <I>diameter</I>
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settings, they are interpreted in the following way.
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</P>
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<P>If "vx", for example, is used as the <I>color</I> setting, then the color
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of the atom will depend on the x-component of its velocity. The
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association of a per-atom value with a specific color is determined by
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a "color map", which can be specified via the
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<A HREF = "dump_modify.html">dump_modify</A> command. The basic idea is that the
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atom-attribute will be within a range of values, and every value
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within the range is mapped to a specific color. Depending on how the
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color map is defined, that mapping can take place via interpolation so
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that a value of -3.2 is halfway between "red" and "blue", or
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discretely so that the value of -3.2 is "orange".
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</P>
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<P>If "vx", for example, is used as the <I>diameter</I> setting, then the atom
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will be rendered using the x-component of its velocity as the
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diameter. If the per-atom value <= 0.0, them the atom will not be
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drawn. Note that finite-size spherical particles, as defined by
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<A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius or
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diameter, which can be used as the <I>diameter</I> setting.
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</P>
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<HR>
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<P>The various kewords listed above control how the image is rendered.
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As listed below, all of the keywords have defaults, most of which you
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will likely not need to change. The <A HREF = "dump_modify.html">dump modify</A>
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also has options specific to the dump image style, particularly for
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assigning colors to atoms, bonds, and other image features.
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</P>
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<HR>
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<P>The <I>adiam</I> keyword allows you to override the <I>diameter</I> setting to a
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per-atom attribute with a specified numeric value. All atoms will be
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drawn with that diameter, e.g. 1.5, which is in whatever distance
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<A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
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</P>
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<P>The <I>atom</I> keyword allow you to turn off the drawing of all atoms,
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if the specified value is <I>no</I>.
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</P>
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<P>The <I>bond</I> keyword allows to you to alter how bonds are drawn. A bond
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is only drawn if both atoms in the bond are being drawn due to being
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in the specified group and due to other selection criteria
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(e.g. region, threshhold settings of the
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<A HREF = "dump_modify.html">dump_modify</A> command). By default, bonds are drawn
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if they are defined in the input data file as read by the
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<A HREF = "read_data.html">read_data</A> command. Using <I>none</I> for both the bond
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<I>color</I> and <I>width</I> value will turn off the drawing of all bonds.
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</P>
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<P>If <I>atom</I> is specified for the bond <I>color</I> value, then each bond is
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drawn in 2 halves, with the color of each half being the color of the
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atom at that end of the bond.
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</P>
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<P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
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bond is determined by its bond type. By default the mapping of bond
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types to colors is as follows:
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</P>
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<UL><LI>type 1 = red
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<LI>type 2 = green
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<LI>type 3 = blue
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<LI>type 4 = yellow
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<LI>type 5 = aqua
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<LI>type 6 = cyan
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</UL>
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<P>and repeats itself for bond types > 6. This mapping can be changed by
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the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
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</P>
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<P>The bond <I>width</I> value can be a numeric value or <I>atom</I> or <I>type</I> (or
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<I>none</I> as indicated above).
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</P>
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<P>If a numeric value is specified, then all bonds will be drawn as
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cylinders with that diameter, e.g. 1.0, which is in whatever distance
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<A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
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</P>
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<P>If <I>atom</I> is specified for the <I>width</I> value, then each bond
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will be drawn with a width corresponding to the minimum diameter
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of the 2 atoms in the bond.
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</P>
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<P>If <I>type</I> is specified for the <I>width</I> value then the diameter of each
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bond is determined by its bond type. By default all types have
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diameter 0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
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bdiam</A> command.
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</P>
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<HR>
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<P>The <I>size</I> keyword sets the width and height of the created images,
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i.e. the number of pixels in each direction.
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</P>
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<HR>
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<P>The <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values determine how
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3d simulation space is mapped to the 2d plane of the image. Basically
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they control how the simulation box appears in the image.
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</P>
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<P>All of the <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values can be
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specified as numeric quantities, whose meaning is explained below.
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Any of them can also be specified as an <A HREF = "variable.html">equal-style
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variable</A>, by using v_name as the value, where "name" is
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the variable name. In this case the variable will be evaluated on the
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timestep each image is created to create a new value. If the
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equal-style variable is time-dependent, this is a means of changing
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the way the simulation box appears from image to image, effectively
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doing a pan or fly-by view of your simulation.
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</P>
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<P>The <I>view</I> keyword determines the viewpoint from which the simulation
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box is viewed, looking towards the <I>center</I> point. The <I>theta</I> value
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is the vertical angle from the +z axis, and must be an angle from 0 to
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180 degrees. The <I>phi</I> value is an azimuthal angle around the z axis
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and can be positive or negative. A value of 0.0 is a view along the
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+x axis, towards the <I>center</I> point. If <I>theta</I> or <I>phi</I> are
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specified via variables, then the variable values should be in
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degrees.
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</P>
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<P>The <I>center</I> keyword determines the point in simulation space that
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will be at the center of the image. <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are
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speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
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the center of the simulation box. These values do not have to be
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between 0.0 and 1.0, if you want the simulation box to be offset from
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the center of the image. Note, however, that if you choose strange
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values for <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally,
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<I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space.
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If <I>flag</I> is set to "s" for static, then this conversion is done once,
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at the time the dump command is issued. If <I>flag</I> is set to "d" for
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dynamic then the conversion is performed every time a new image is
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created. If the box size or shape is changing, this will adjust the
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center point in simulation space.
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</P>
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<P>The <I>up</I> keyword determines what direction in simulation space will be
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"up" in the image. Internally it is stored as a vector that is in the
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plane perpendicular to the view vector implied by the <I>theta</I> and
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<I>pni</I> values, and which is also in the plane defined by the view
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vector and user-specified up vector. Thus this internal vector is
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computed from the user-specified <I>up</I> vector as
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</P>
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<PRE>up_internal = view cross (up cross view)
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</PRE>
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<P>This means the only restriction on the specified <I>up</I> vector is that
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it cannot be parallel to the <I>view</I> vector, implied by the <I>theta</I> and
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<I>phi</I> values.
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</P>
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<P>The <I>zoom</I> keyword scales the size of the simulation box as it appears
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in the image. The default <I>zfactor</I> value of 1 should display an
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image mostly filled by the atoms in the simulation box. A <I>zfactor</I> >
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1 will make the simulation box larger; a <I>zfactor</I> < 1 will make it
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smaller. <I>Zfactor</I> must be a value > 0.0.
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</P>
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<P>The <I>persp</I> keyword determines how much depth perspective is present
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in the image. Depth perspective makes lines that are parallel in
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simulation space appear non-parallel in the image. A <I>pfactor</I> value
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of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
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which is an orthographic rendering with no persepctive. A <I>pfactor</I>
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value between 0.0 and 1.0 will introduce more perspective. A <I>pfactor</I>
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value > 1 will create a highly skewed image with a large amount of
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perspective.
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</P>
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<P>IMPORTANT NOTE: The <I>persp</I> keyword is not yet supported as an option.
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</P>
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<HR>
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<P>The <I>box</I> keyword determines how the simulation box boundaries are
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rendered as thin cylinders in the image. If <I>no</I> is set, then the box
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boundaries are not drawn and the <I>diam</I> setting is ignored. If <I>yes</I>
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is set, the 12 edges of the box are drawn, with a diameter that is a
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fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
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The color of the box boundaries can be set with the <A HREF = "dump_modify.html">dump_modify
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boxcolor</A> command.
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</P>
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<P>The <I>axes</I> keyword determines how the coordinate axes are rendered as
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thin cylinders in the image. If <I>no</I> is set, then the axes are not
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drawn and the <I>length</I> and <I>diam</I> settings are ignored. If <I>yes</I> is
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set, 3 thin cylinders are drawn to represent the x,y,z axes in colors
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red,green,blue. The origin of these cylinders will be offset from the
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lower left corner of the box by 10%. The <I>length</I> setting determines
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how long the cylinders will be as a fraction of the respective box
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lengths. The <I>diam</I> setting determines their thickness as a fraction
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of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
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</P>
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<HR>
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<P>The <I>shiny</I> keyword determines how shiny the objects rendered in the
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image will appear. The <I>sfactor</I> value must be a value 0.0 <=
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<I>sfactor</I> <= 1.0, where <I>sfactor</I> = 1 is a highly reflective surface
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and <I>sfactor</I> = 0 is a rough non-shiny surface.
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</P>
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<P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion
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(SSAO) model for depth shading. If <I>yes</I> is set, then atoms further
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away from the viewer are darkened via a randomized process, which is
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perceived as depth. The calculation of this effect can increase the
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cost of computing the image by roughly 2x. The strength of the effect
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can be scaled by the <I>dfactor</I> parameter. If <I>no</I> is set, no depth
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shading is performed.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>A series of JPG or PPM images can be converted into a movie file and
|
|
then played as a movie using commonly available tools.
|
|
</P>
|
|
<P>Convert JPG or PPM files into an animated GIF or MPEG or other movie
|
|
file:
|
|
</P>
|
|
<UL><LI>a) Use the ImageMagick convert program.
|
|
|
|
<PRE>% convert *.jpg foo.gif
|
|
% convert -loop 1 *.ppm foo.mpg
|
|
</PRE>
|
|
<LI>b) Use QuickTime.
|
|
|
|
<P>Select "Open Image Sequence" under the File menu
|
|
Load the images into QuickTime to animate them
|
|
Select "Export" under the File menu
|
|
Save the movie as a QuickTime movie (*.mov) or in another format
|
|
</P>
|
|
<LI>c) Windows-based tool.
|
|
</UL>
|
|
<P>If someone tells us how to do this via a common Windows-based tool,
|
|
we'll post the instructions here.
|
|
</P>
|
|
<P>Play the movie:
|
|
</P>
|
|
<UL><LI>a) Use your browser to view an animated GIF movie.
|
|
|
|
<P>Select "Open File" under the File menu
|
|
Load the animated GIF file
|
|
</P>
|
|
<LI>b) Use the freely available mplayer tool to view an MPEG movie.
|
|
|
|
<PRE>% mplayer foo.mpg
|
|
</PRE>
|
|
<LI>c) Use the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>
|
|
<A HREF = "http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</A>,
|
|
which works directly on a series of image files.
|
|
|
|
<PRE>a = animate("foo*.jpg")
|
|
</PRE>
|
|
<LI>d) QuickTime and other Windows-based media players can
|
|
obviously play movie files directly.
|
|
</UL>
|
|
<HR>
|
|
|
|
<P>See <A HREF = "Section_modify.html">Section_modify</A> of the manual for information
|
|
on how to add new compute and fix styles to LAMMPS to calculate
|
|
per-atom quantities which could then be output into dump files.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>To write JPG images, you must use a -DLAMMPS_JPEG switch when building
|
|
LAMMPS and link with a JPEG library. See the <A HREF = "Section_start.html#start_2_4">Making
|
|
LAMMPS</A> section of the documentation for
|
|
details.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "undump.html">undump</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The defaults for the keywords are as follows:
|
|
</P>
|
|
<UL><LI>adiam = not specified (use diameter setting)
|
|
<LI>atom = yes
|
|
<LI>bond = none none (if no bonds in system)
|
|
<LI>bond = atom 0.5 (if bonds in system)
|
|
<LI>size = 512 512
|
|
<LI>view = 60 30 (for 3d)
|
|
<LI>view = 0 0 (for 2d)
|
|
<LI>center = s 0.5 0.5 0.5
|
|
<LI>up = 0 0 1 (for 3d)
|
|
<LI>up = 0 1 0 (for 2d)
|
|
<LI>zoom = 1.0
|
|
<LI>persp = 0.0
|
|
<LI>box = yes 0.02
|
|
<LI>axes = no 0.0 0.0
|
|
<LI>shiny = 1.0
|
|
<LI>ssao = no
|
|
</UL>
|
|
</HTML>
|