forked from lijiext/lammps
512 lines
22 KiB
Plaintext
512 lines
22 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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dump image command :h3
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dump movie command :h3
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[Syntax:]
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dump ID group-ID style N file color diameter keyword value ... :pre
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ID = user-assigned name for the dump :ulb,l
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group-ID = ID of the group of atoms to be imaged :l
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style = {image} or {movie} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
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N = dump every this many timesteps :l
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file = name of file to write image to :l
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color = atom attribute that determines color of each atom :l
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diameter = atom attribute that determines size of each atom :l
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zero or more keyword/value pairs may be appended :l
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keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
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{adiam} value = number = numeric value for atom diameter (distance units)
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{atom} = yes/no = do or do not draw atoms
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{bond} values = color width = color and width of bonds
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color = {atom} or {type} or {none}
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width = number or {atom} or {type} or {none}
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number = numeric value for bond width (distance units)
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{size} 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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{view} 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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{center} 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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{up} 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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{zoom} 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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{persp} 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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{box} 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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{axes} 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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{shiny} 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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{ssao} 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 :pre
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:ule
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[Examples:]
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dump d0 all image 100 dump.*.jpg type type
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dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
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dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
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dump m0 all movie 1000 movie.mpg type type size 640 480
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dump m1 all movie 1000 movie.avi type type size 640 480
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dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 :pre
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[Description:]
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Dump a high-quality rendered image of the atom configuration every N
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timesteps and save the images either as a sequence of JPG or PNG, or
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PPM files, or as a single movie file. The options for this command as
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well as the "dump_modify"_dump_modify.html command control what is
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included in the image or movie and how it appears. A series of such
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images can easily be manually converted into an animated movie of your
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simulation or the process can be automated without writing the
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intermediate files using the dump movie style; see further details
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below. Other dump styles store snapshots of numerical data asociated
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with atoms in various formats, as discussed on the "dump"_dump.html
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doc page.
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Note that a set of images or a movie can be made after a simulation
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has been run, using the "rerun"_rerun.html command to read snapshots
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from an existing dump file, and using these dump commands in the rerun
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script to generate the images/movie.
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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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<DIV ALIGN=center>
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:image(JPG/dump1_small.jpg,JPG/dump1.jpg)
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:image(JPG/dump2_small.jpg,JPG/dump2.jpg)
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</DIV>
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Only atoms in the specified group are rendered in the image. The
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"dump_modify region and thresh"_dump_modify.html commands can also
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alter what atoms are included in the image.\
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The filename suffix determines whether a JPEG, PNG, or PPM file is
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created with the {image} dump style. If the suffix is ".jpg" or ".jpeg",
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then a JPEG format file is created, if the suffix is ".png", then a PNG
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format is created, else a PPM (aka NETPBM) format file is created.
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The JPG and PNG files are binary; PPM has a text mode header followed
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by binary data. JPG images have lossy compression; PNG has lossless
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compression; and PPM files are uncompressed but can be compressed with
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gzip, if LAMMPS has been compiled with -DLAMMPS_GZIP and a ".gz" suffix
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is used.
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Similarly, the format of the resulting movie is chosen with the
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{movie} dump style. This is handled by the underlying FFmpeg converter
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and thus details have to be looked up in the FFmpeg documentation.
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Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
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Additional settings of the movie compression like bitrate and
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framerate can be set using the "dump_modify"_dump_modify.html command.
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To write out JPEG and PNG format files, you must build LAMMPS with
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support for the corresponding JPEG or PNG library. To convert images
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into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
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flag. See "this section"_Section_start.html#start_2_4 of the manual
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for instructions on how to do this.
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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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:line
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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 "dump_modify first"_dump_modify.html 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 "dump_modify every"_dump_modify.html command.
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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 "dump_modify pad"_dump_modify.html 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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Dump {movie} filenames on the other hand, must not have any wildcard
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character since only one file combining all images into a single
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movie will be written by the movie encoder.
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:line
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The {color} and {diameter} 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 "dump custom"_dump.html command, including {type} and
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{element}. This includes per-atom quantities calculated by a
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"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html,
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which are prefixed by "c_", "f_", or "v_" respectively. Note that the
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{diameter} setting can be overridden with a numeric value by the
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optional {adiam} keyword, in which case you can specify the {diameter}
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setting with any valid atom attribute.
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If {type} is specified for the {color} 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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type 1 = red
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type 2 = green
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type 3 = blue
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type 4 = yellow
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type 5 = aqua
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type 6 = cyan :ul
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and repeats itself for types > 6. This mapping can be changed by the
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"dump_modify acolor"_dump_modify.html command.
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If {type} is specified for the {diameter} 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 "dump_modify
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adiam"_dump_modify.html command.
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If {element} is specified for the {color} and/or {diameter} 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 "AtomEye"_atomeye visualization package.
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:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
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If other atom attributes are used for the {color} or {diameter}
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settings, they are interpreted in the following way.
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If "vx", for example, is used as the {color} 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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"dump_modify"_dump_modify.html 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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If "vx", for example, is used as the {diameter} 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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"atom_style sphere"_atom_style.html define a per-particle radius or
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diameter, which can be used as the {diameter} setting.
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:line
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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 "dump modify"_dump_modify.html
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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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:line
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The {adiam} keyword allows you to override the {diameter} 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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"units"_units.html the input script defines, e.g. Angstroms.
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The {atom} keyword allow you to turn off the drawing of all atoms,
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if the specified value is {no}.
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The {bond} 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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"dump_modify"_dump_modify.html 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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"read_data"_read_data.html command. Using {none} for both the bond
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{color} and {width} value will turn off the drawing of all bonds.
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If {atom} is specified for the bond {color} 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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If {type} is specified for the {color} 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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type 1 = red
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type 2 = green
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type 3 = blue
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type 4 = yellow
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type 5 = aqua
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type 6 = cyan :ul
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and repeats itself for bond types > 6. This mapping can be changed by
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the "dump_modify bcolor"_dump_modify.html command.
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The bond {width} value can be a numeric value or {atom} or {type} (or
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{none} as indicated above).
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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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"units"_units.html the input script defines, e.g. Angstroms.
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If {atom} is specified for the {width} 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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If {type} is specified for the {width} 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 "dump_modify
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bdiam"_dump_modify.html command.
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:line
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The {size} 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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:line
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The {view}, {center}, {up}, {zoom}, and {persp} 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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All of the {view}, {center}, {up}, {zoom}, and {persp} 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 "equal-style
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variable"_variable.html, 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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The {view} keyword determines the viewpoint from which the simulation
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box is viewed, looking towards the {center} point. The {theta} 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 {phi} 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 {center} point. If {theta} or {phi} are
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specified via variables, then the variable values should be in
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degrees.
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The {center} keyword determines the point in simulation space that
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will be at the center of the image. {Cx}, {Cy}, and {Cz} 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 {Cx}, {Cy}, or {Cz} you may get a blank image. Internally,
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{Cx}, {Cy}, and {Cz} are converted into a point in simulation space.
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If {flag} 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 {flag} 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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The {up} 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 {theta} and
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{pni} 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 {up} vector as
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up_internal = view cross (up cross view) :pre
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This means the only restriction on the specified {up} vector is that
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it cannot be parallel to the {view} vector, implied by the {theta} and
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{phi} values.
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The {zoom} keyword scales the size of the simulation box as it appears
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in the image. The default {zfactor} value of 1 should display an
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image mostly filled by the atoms in the simulation box. A {zfactor} >
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1 will make the simulation box larger; a {zfactor} < 1 will make it
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smaller. {Zfactor} must be a value > 0.0.
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The {persp} 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 {pfactor} 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 {pfactor}
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value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
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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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IMPORTANT NOTE: The {persp} keyword is not yet supported as an option.
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:line
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The {box} keyword determines how the simulation box boundaries are
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rendered as thin cylinders in the image. If {no} is set, then the box
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boundaries are not drawn and the {diam} setting is ignored. If {yes}
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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 "dump_modify
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boxcolor"_dump_modify.html command.
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The {axes} keyword determines how the coordinate axes are rendered as
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thin cylinders in the image. If {no} is set, then the axes are not
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drawn and the {length} and {diam} settings are ignored. If {yes} 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 {length} 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 {diam} 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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:line
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The {shiny} keyword determines how shiny the objects rendered in the
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image will appear. The {sfactor} value must be a value 0.0 <=
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{sfactor} <= 1.0, where {sfactor} = 1 is a highly reflective surface
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and {sfactor} = 0 is a rough non-shiny surface.
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The {ssao} keyword turns on/off a screen space ambient occlusion
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(SSAO) model for depth shading. If {yes} 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 {dfactor} parameter. If {no} is set, no depth
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shading is performed.
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:line
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A series of JPG, PNG, or PPM images can be converted into a movie file
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and then played as a movie using commonly available tools. Using dump
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style {movie} automates this step and avoids the intermediate step of
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writing (many) image snapshot file. But LAMMPS has to be compiled with
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-DLAMMPS_FFMPEG and an FFmpeg executable have to be installed.
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To manually convert JPG, PNG or PPM files into an animated GIF or MPEG
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or other movie file you can use:
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a) Use the ImageMagick convert program. :ulb,l
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% convert *.jpg foo.gif
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% convert -loop 1 *.ppm foo.mpg :pre
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Animated GIF files from ImageMagick are unoptimized. You can use a
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program like gifsicle to optimize and massively shrink them.
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MPEG files created by ImageMagick are in MPEG-1 format with rather
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inefficient compression and low quality.
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b) Use QuickTime. :l
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Select "Open Image Sequence" under the File menu Load the images into
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QuickTime to animate them Select "Export" under the File menu Save the
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movie as a QuickTime movie (*.mov) or in another format. QuickTime
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can generate very high quality and efficiently compressed movie
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files. Some of the supported formats require to buy a license and some
|
|
are not readable on all platforms until specific runtime libraries are
|
|
installed.
|
|
|
|
c) Use FFmpeg :l
|
|
|
|
FFmpeg is a command line tool that is available on many platforms and
|
|
allows extremely flexible encoding and decoding of movies.
|
|
|
|
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
|
|
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre
|
|
|
|
Frontends for FFmpeg exist for multiple platforms. For more
|
|
information see the "FFmpeg homepage"_http://www.ffmpeg.org/
|
|
|
|
:ule
|
|
|
|
:line
|
|
|
|
Play the movie:
|
|
|
|
a) Use your browser to view an animated GIF movie. :ulb,l
|
|
|
|
Select "Open File" under the File menu
|
|
Load the animated GIF file
|
|
|
|
b) Use the freely available mplayer or ffplay tool to view a
|
|
movie. Both are available for multiple OSes and support a large
|
|
variety of file formats and decoders. :l
|
|
|
|
% mplayer foo.mpg
|
|
% ffplay bar.avi :pre
|
|
|
|
c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html
|
|
"animate tool"_http://www.sandia.gov/~sjplimp/pizza/doc/animate.html,
|
|
which works directly on a series of image files. :l
|
|
|
|
a = animate("foo*.jpg") :pre
|
|
|
|
d) QuickTime and other Windows- or MacOS-based media players can
|
|
obviously play movie files directly. Similarly for corresponding tools
|
|
bundled with Linux desktop environments. However, due to licensing
|
|
issues with some file formats, the formats may require installing
|
|
additional libraries, purchasing a license, or may not be
|
|
supported. :ule,l
|
|
|
|
:line
|
|
|
|
See "Section_modify"_Section_modify.html 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.
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
To write JPG images, you must use the -DLAMMPS_JPEG switch when
|
|
building LAMMPS and link with a JPEG library. To write PNG images, you
|
|
must use the -DLAMMPS_PNG switch when building LAMMPS and link with a
|
|
PNG library.
|
|
|
|
To write {movie} dumps, you must use the -DLAMMPS_FFMPEG switch when
|
|
building LAMMPS and have the FFmpeg executable available on the
|
|
machine where LAMMPS is being run.
|
|
|
|
See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
|
|
documentation for details on how to configure and compile optional in
|
|
LAMMPS.
|
|
|
|
[Related commands:]
|
|
|
|
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
|
|
|
|
[Default:]
|
|
|
|
The defaults for the keywords are as follows:
|
|
|
|
adiam = not specified (use diameter setting)
|
|
atom = yes
|
|
bond = none none (if no bonds in system)
|
|
bond = atom 0.5 (if bonds in system)
|
|
size = 512 512
|
|
view = 60 30 (for 3d)
|
|
view = 0 0 (for 2d)
|
|
center = s 0.5 0.5 0.5
|
|
up = 0 0 1 (for 3d)
|
|
up = 0 1 0 (for 2d)
|
|
zoom = 1.0
|
|
persp = 0.0
|
|
box = yes 0.02
|
|
axes = no 0.0 0.0
|
|
shiny = 1.0
|
|
ssao = no :ul
|