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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>dump image command</li>
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<a href="Section_commands.html#comm">Commands</a>
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<div class="section" id="dump-image-command">
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<span id="index-0"></span><h1>dump image command<a class="headerlink" href="#dump-image-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="dump-movie-command">
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<h1>dump movie command<a class="headerlink" href="#dump-movie-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>dump ID group-ID style N file color diameter keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID = user-assigned name for the dump</li>
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<li>group-ID = ID of the group of atoms to be imaged</li>
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<li>style = <em>image</em> or <em>movie</em> = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a> doc page)</li>
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<li>N = dump every this many timesteps</li>
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<li>file = name of file to write image to</li>
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<li>color = atom attribute that determines color of each atom</li>
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<li>diameter = atom attribute that determines size of each atom</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
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</ul>
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<pre class="literal-block">
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<em>atom</em> = yes/no = do or do not draw atoms
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<em>adiam</em> size = numeric value for atom diameter (distance units)
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<em>bond</em> values = color width = color and width of bonds
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color = <em>atom</em> or <em>type</em> or <em>none</em>
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width = number or <em>atom</em> or <em>type</em> or <em>none</em>
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number = numeric value for bond width (distance units)
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<em>line</em> = color width
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color = <em>type</em>
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width = numeric value for line width (distance units)
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<em>tri</em> = color tflag width
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color = <em>type</em>
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tflag = 1 for just triangle, 2 for just tri edges, 3 for both
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width = numeric value for tringle edge width (distance units)
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<em>body</em> = color bflag1 bflag2
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color = <em>type</em>
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bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
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<em>size</em> 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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<em>view</em> 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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<em>center</em> 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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<em>up</em> 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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<em>zoom</em> 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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<em>persp</em> 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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<em>box</em> 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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<em>axes</em> 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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<em>subbox</em> values = yes/no diam = draw outline of processor sub-domains
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yes/no = do or do not draw sub-domain lines
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diam = diameter of sub-domain lines as fraction of shortest box length
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<em>shiny</em> 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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<em>ssao</em> 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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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>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
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>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 JPEG 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 <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> 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 <a class="reference internal" href="dump.html"><em>dump</em></a>
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doc page.</p>
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<p>Note that a set of images or a movie can be made after a simulation
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has been run, using the <a class="reference internal" href="rerun.html"><em>rerun</em></a> 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.</p>
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<p>Here are two sample images, rendered as 1024x1024 JPEG files. Click
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to see the full-size images:</p>
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<DIV ALIGN=center><a data-lightbox="group-default"
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href="_images/dump1.jpg"
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class=""
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title=""
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data-title=""
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><img src="_images/dump1.jpg"
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class=""
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width="25%"
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height="auto"
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alt=""/>
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</a><a data-lightbox="group-default"
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href="_images/dump2.jpg"
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class=""
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title=""
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data-title=""
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><img src="_images/dump2.jpg"
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class=""
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width="25%"
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height="auto"
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alt=""/>
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</a></DIV><p>Only atoms in the specified group are rendered in the image. The
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<a class="reference internal" href="dump_modify.html"><em>dump_modify region and thresh</em></a> 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 <em>image</em> dump style. If the suffix is ”.jpg” or
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”.jpeg”, then a JPEG format file is created, if the suffix is ”.png”,
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then a PNG format is created, else a PPM (aka NETPBM) format file is
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created. The JPEG and PNG files are binary; PPM has a text mode
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header followed by binary data. JPEG images have lossy compression;
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PNG has lossless compression; and PPM files are uncompressed but can
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be compressed with gzip, if LAMMPS has been compiled with
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-DLAMMPS_GZIP and a ”.gz” suffix is used.</p>
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<p>Similarly, the format of the resulting movie is chosen with the
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<em>movie</em> 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 <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
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<p>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 <a class="reference internal" href="Section_start.html#start-2-4"><span>this section</span></a> of the manual
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for instructions on how to do this.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Because periodic boundary conditions are enforced only on
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timesteps when neighbor lists are rebuilt, the coordinates of an atom
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in the image may be slightly outside the simulation box.</p>
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</div>
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<hr class="docutils" />
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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 class="reference internal" href="dump_modify.html"><em>dump_modify first</em></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 class="reference internal" href="dump_modify.html"><em>dump_modify every</em></a> command.</p>
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<p>Dump <em>image</em> 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 class="reference internal" href="dump_modify.html"><em>dump_modify pad</em></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.</p>
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<p>Dump <em>movie</em> 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.</p>
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<hr class="docutils" />
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<p>The <em>color</em> and <em>diameter</em> 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 class="reference internal" href="dump.html"><em>dump custom</em></a> command, including <em>type</em> and
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<em>element</em>. This includes per-atom quantities calculated by a
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<a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, or <a class="reference internal" href="variable.html"><em>variable</em></a>,
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which are prefixed by “<a href="#id9"><span class="problematic" id="id10">c_</span></a>”, “<a href="#id11"><span class="problematic" id="id12">f_</span></a>”, or “<a href="#id13"><span class="problematic" id="id14">v_</span></a>” respectively. Note that the
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<em>diameter</em> setting can be overridden with a numeric value applied to
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all atoms by the optional <em>adiam</em> keyword.</p>
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<p>If <em>type</em> is specified for the <em>color</em> 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:</p>
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<ul class="simple">
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<li>type 1 = red</li>
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<li>type 2 = green</li>
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<li>type 3 = blue</li>
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<li>type 4 = yellow</li>
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<li>type 5 = aqua</li>
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<li>type 6 = cyan</li>
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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 class="reference internal" href="dump_modify.html"><em>dump_modify acolor</em></a> command.</p>
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<p>If <em>type</em> is specified for the <em>diameter</em> 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 class="reference internal" href="dump_modify.html"><em>dump_modify adiam</em></a> command.</p>
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<p>If <em>element</em> is specified for the <em>color</em> and/or <em>diameter</em> 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 class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualization package.</p>
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<p>If other atom attributes are used for the <em>color</em> or <em>diameter</em>
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settings, they are interpreted in the following way.</p>
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<p>If “vx”, for example, is used as the <em>color</em> 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 class="reference internal" href="dump_modify.html"><em>dump_modify</em></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”.</p>
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<p>If “vx”, for example, is used as the <em>diameter</em> 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 class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> define a per-particle radius or
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diameter, which can be used as the <em>diameter</em> setting.</p>
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<hr class="docutils" />
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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 class="reference internal" href="dump_modify.html"><em>dump modify</em></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.</p>
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<hr class="docutils" />
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<p>The <em>atom</em> keyword allow you to turn off the drawing of all atoms, if
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the specified value is <em>no</em>. Note that this will not turn off the
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drawing of particles that are represented as lines, triangles, or
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bodies, as discussed below. These particles can be drawn separately
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if the <em>line</em>, <em>tri</em>, or <em>body</em> keywords are used.</p>
|
|
<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to
|
|
set a single numeric <em>size</em>. All atoms will be drawn with that
|
|
diameter, e.g. 1.5, which is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a>
|
|
the input script defines, e.g. Angstroms.</p>
|
|
<p>The <em>bond</em> keyword allows to you to alter how bonds are drawn. A bond
|
|
is only drawn if both atoms in the bond are being drawn due to being
|
|
in the specified group and due to other selection criteria
|
|
(e.g. region, threshhold settings of the
|
|
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command). By default, bonds are drawn
|
|
if they are defined in the input data file as read by the
|
|
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Using <em>none</em> for both the bond
|
|
<em>color</em> and <em>width</em> value will turn off the drawing of all bonds.</p>
|
|
<p>If <em>atom</em> is specified for the bond <em>color</em> value, then each bond is
|
|
drawn in 2 halves, with the color of each half being the color of the
|
|
atom at that end of the bond.</p>
|
|
<p>If <em>type</em> is specified for the <em>color</em> value, then the color of each
|
|
bond is determined by its bond type. By default the mapping of bond
|
|
types to colors is as follows:</p>
|
|
<ul class="simple">
|
|
<li>type 1 = red</li>
|
|
<li>type 2 = green</li>
|
|
<li>type 3 = blue</li>
|
|
<li>type 4 = yellow</li>
|
|
<li>type 5 = aqua</li>
|
|
<li>type 6 = cyan</li>
|
|
</ul>
|
|
<p>and repeats itself for bond types > 6. This mapping can be changed by
|
|
the <a class="reference internal" href="dump_modify.html"><em>dump_modify bcolor</em></a> command.</p>
|
|
<p>The bond <em>width</em> value can be a numeric value or <em>atom</em> or <em>type</em> (or
|
|
<em>none</em> as indicated above).</p>
|
|
<p>If a numeric value is specified, then all bonds will be drawn as
|
|
cylinders with that diameter, e.g. 1.0, which is in whatever distance
|
|
<a class="reference internal" href="units.html"><em>units</em></a> the input script defines, e.g. Angstroms.</p>
|
|
<p>If <em>atom</em> is specified for the <em>width</em> value, then each bond
|
|
will be drawn with a width corresponding to the minimum diameter
|
|
of the 2 atoms in the bond.</p>
|
|
<p>If <em>type</em> is specified for the <em>width</em> value then the diameter of each
|
|
bond is determined by its bond type. By default all types have
|
|
diameter 0.5. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><em>dump_modify bdiam</em></a> command.</p>
|
|
<p>The <em>line</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a>
|
|
is used to define particles as line segments, and will draw them as
|
|
lines. If this keyword is not used, such particles will be drawn as
|
|
spheres, the same as if they were regular atoms. The only setting
|
|
currently allowed for the <em>color</em> value is <em>type</em>, which will color
|
|
the lines according to the atom type of the particle. By default the
|
|
mapping of types to colors is as follows:</p>
|
|
<ul class="simple">
|
|
<li>type 1 = red</li>
|
|
<li>type 2 = green</li>
|
|
<li>type 3 = blue</li>
|
|
<li>type 4 = yellow</li>
|
|
<li>type 5 = aqua</li>
|
|
<li>type 6 = cyan</li>
|
|
</ul>
|
|
<p>and repeats itself for types > 6. There is not yet an option to
|
|
change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
|
|
<p>The line <em>width</em> can only be a numeric value, which specifies that all
|
|
lines will be drawn as cylinders with that diameter, e.g. 1.0, which
|
|
is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a> the input script defines,
|
|
e.g. Angstroms.</p>
|
|
<p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> is
|
|
used to define particles as triangles, and will draw them as triangles
|
|
or edges (3 lines) or both, depending on the setting for <em>tflag</em>. If
|
|
edges are drawn, the <em>width</em> setting determines the diameters of the
|
|
line segments. If this keyword is not used, triangle particles will
|
|
be drawn as spheres, the same as if they were regular atoms. The only
|
|
setting currently allowed for the <em>color</em> value is <em>type</em>, which will
|
|
color the triangles according to the atom type of the particle. By
|
|
default the mapping of types to colors is as follows:</p>
|
|
<ul class="simple">
|
|
<li>type 1 = red</li>
|
|
<li>type 2 = green</li>
|
|
<li>type 3 = blue</li>
|
|
<li>type 4 = yellow</li>
|
|
<li>type 5 = aqua</li>
|
|
<li>type 6 = cyan</li>
|
|
</ul>
|
|
<p>and repeats itself for types > 6. There is not yet an option to
|
|
change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
|
|
<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
|
|
is used to define body particles with internal state
|
|
(e.g. sub-particles), and will drawn them in a manner specific to the
|
|
body style. If this keyword is not used, such particles will be drawn
|
|
as spheres, the same as if they were regular atoms.</p>
|
|
<p>The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body styles LAMMPS
|
|
currently supports, and provides more details as to the kind of body
|
|
particles they represent and how they are drawn by this dump image
|
|
command. For all the body styles, individual atoms can be either a
|
|
body particle or a usual point (non-body) particle. Non-body
|
|
particles will be drawn the same way they would be as a regular atom.
|
|
The <em>bflag1</em> and <em>bflag2</em> settings are numerical values which are
|
|
passed to the body style to affect how the drawing of a body particle
|
|
is done. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for a description of what
|
|
these parameters mean for each body style.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>size</em> keyword sets the width and height of the created images,
|
|
i.e. the number of pixels in each direction.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values determine how
|
|
3d simulation space is mapped to the 2d plane of the image. Basically
|
|
they control how the simulation box appears in the image.</p>
|
|
<p>All of the <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values can be
|
|
specified as numeric quantities, whose meaning is explained below.
|
|
Any of them can also be specified as an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>, by using v_name as the value, where “name” is
|
|
the variable name. In this case the variable will be evaluated on the
|
|
timestep each image is created to create a new value. If the
|
|
equal-style variable is time-dependent, this is a means of changing
|
|
the way the simulation box appears from image to image, effectively
|
|
doing a pan or fly-by view of your simulation.</p>
|
|
<p>The <em>view</em> keyword determines the viewpoint from which the simulation
|
|
box is viewed, looking towards the <em>center</em> point. The <em>theta</em> value
|
|
is the vertical angle from the +z axis, and must be an angle from 0 to
|
|
180 degrees. The <em>phi</em> value is an azimuthal angle around the z axis
|
|
and can be positive or negative. A value of 0.0 is a view along the
|
|
+x axis, towards the <em>center</em> point. If <em>theta</em> or <em>phi</em> are
|
|
specified via variables, then the variable values should be in
|
|
degrees.</p>
|
|
<p>The <em>center</em> keyword determines the point in simulation space that
|
|
will be at the center of the image. <em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are
|
|
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
|
|
the center of the simulation box. These values do not have to be
|
|
between 0.0 and 1.0, if you want the simulation box to be offset from
|
|
the center of the image. Note, however, that if you choose strange
|
|
values for <em>Cx</em>, <em>Cy</em>, or <em>Cz</em> you may get a blank image. Internally,
|
|
<em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are converted into a point in simulation space.
|
|
If <em>flag</em> is set to “s” for static, then this conversion is done once,
|
|
at the time the dump command is issued. If <em>flag</em> is set to “d” for
|
|
dynamic then the conversion is performed every time a new image is
|
|
created. If the box size or shape is changing, this will adjust the
|
|
center point in simulation space.</p>
|
|
<p>The <em>up</em> keyword determines what direction in simulation space will be
|
|
“up” in the image. Internally it is stored as a vector that is in the
|
|
plane perpendicular to the view vector implied by the <em>theta</em> and
|
|
<em>pni</em> values, and which is also in the plane defined by the view
|
|
vector and user-specified up vector. Thus this internal vector is
|
|
computed from the user-specified <em>up</em> vector as</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>up_internal = view cross (up cross view)
|
|
</pre></div>
|
|
</div>
|
|
<p>This means the only restriction on the specified <em>up</em> vector is that
|
|
it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
|
|
<em>phi</em> values.</p>
|
|
<p>The <em>zoom</em> keyword scales the size of the simulation box as it appears
|
|
in the image. The default <em>zfactor</em> value of 1 should display an
|
|
image mostly filled by the atoms in the simulation box. A <em>zfactor</em> >
|
|
1 will make the simulation box larger; a <em>zfactor</em> < 1 will make it
|
|
smaller. <em>Zfactor</em> must be a value > 0.0.</p>
|
|
<p>The <em>persp</em> keyword determines how much depth perspective is present
|
|
in the image. Depth perspective makes lines that are parallel in
|
|
simulation space appear non-parallel in the image. A <em>pfactor</em> value
|
|
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
|
|
which is an orthographic rendering with no persepctive. A <em>pfactor</em>
|
|
value between 0.0 and 1.0 will introduce more perspective. A <em>pfactor</em>
|
|
value > 1 will create a highly skewed image with a large amount of
|
|
perspective.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The <em>persp</em> keyword is not yet supported as an option.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>box</em> keyword determines if and how the simulation box boundaries
|
|
are rendered as thin cylinders in the image. If <em>no</em> is set, then the
|
|
box boundaries are not drawn and the <em>diam</em> setting is ignored. If
|
|
<em>yes</em> is set, the 12 edges of the box are drawn, with a diameter that
|
|
is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
|
|
2d). The color of the box boundaries can be set with the <a class="reference internal" href="dump_modify.html"><em>dump_modify boxcolor</em></a> command.</p>
|
|
<p>The <em>axes</em> keyword determines if and how the coordinate axes are
|
|
rendered as thin cylinders in the image. If <em>no</em> is set, then the
|
|
axes are not drawn and the <em>length</em> and <em>diam</em> settings are ignored.
|
|
If <em>yes</em> is set, 3 thin cylinders are drawn to represent the x,y,z
|
|
axes in colors red,green,blue. The origin of these cylinders will be
|
|
offset from the lower left corner of the box by 10%. The <em>length</em>
|
|
setting determines how long the cylinders will be as a fraction of the
|
|
respective box lengths. The <em>diam</em> setting determines their thickness
|
|
as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
|
|
2d).</p>
|
|
<p>The <em>subbox</em> keyword determines if and how processor sub-domain
|
|
boundaries are rendered as thin cylinders in the image. If <em>no</em> is
|
|
set (default), then the sub-domain boundaries are not drawn and the
|
|
<em>diam</em> setting is ignored. If <em>yes</em> is set, the 12 edges of each
|
|
processor sub-domain are drawn, with a diameter that is a fraction of
|
|
the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
|
|
of the sub-domain boundaries can be set with the <a class="reference internal" href="dump_modify.html"><em>dump_modify boxcolor</em></a> command.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>shiny</em> keyword determines how shiny the objects rendered in the
|
|
image will appear. The <em>sfactor</em> value must be a value 0.0 <=
|
|
<em>sfactor</em> <= 1.0, where <em>sfactor</em> = 1 is a highly reflective surface
|
|
and <em>sfactor</em> = 0 is a rough non-shiny surface.</p>
|
|
<p>The <em>ssao</em> keyword turns on/off a screen space ambient occlusion
|
|
(SSAO) model for depth shading. If <em>yes</em> is set, then atoms further
|
|
away from the viewer are darkened via a randomized process, which is
|
|
perceived as depth. The calculation of this effect can increase the
|
|
cost of computing the image by roughly 2x. The strength of the effect
|
|
can be scaled by the <em>dfactor</em> parameter. If <em>no</em> is set, no depth
|
|
shading is performed.</p>
|
|
<hr class="docutils" />
|
|
<p>A series of JPEG, PNG, or PPM images can be converted into a movie
|
|
file and then played as a movie using commonly available tools. Using
|
|
dump style <em>movie</em> automates this step and avoids the intermediate
|
|
step of writing (many) image snapshot file. But LAMMPS has to be
|
|
compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be
|
|
installed.</p>
|
|
<p>To manually convert JPEG, PNG or PPM files into an animated GIF or
|
|
MPEG or other movie file you can use:</p>
|
|
<ul class="simple">
|
|
<li><ol class="first loweralpha">
|
|
<li>Use the ImageMagick convert program.</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>% convert *.jpg foo.gif
|
|
% convert -loop 1 *.ppm foo.mpg
|
|
</pre></div>
|
|
</div>
|
|
<p>Animated GIF files from ImageMagick are unoptimized. You can use a
|
|
program like gifsicle to optimize and massively shrink them.
|
|
MPEG files created by ImageMagick are in MPEG-1 format with rather
|
|
inefficient compression and low quality.</p>
|
|
<ul class="simple">
|
|
<li><ol class="first loweralpha" start="2">
|
|
<li>Use QuickTime.</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<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 (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format. QuickTime
|
|
can generate very high quality and efficiently compressed movie
|
|
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.</p>
|
|
<ul class="simple">
|
|
<li><ol class="first loweralpha" start="3">
|
|
<li>Use FFmpeg</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<p>FFmpeg is a command line tool that is available on many platforms and
|
|
allows extremely flexible encoding and decoding of movies.</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>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></div>
|
|
</div>
|
|
<p>Frontends for FFmpeg exist for multiple platforms. For more
|
|
information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
|
|
<hr class="docutils" />
|
|
<p>Play the movie:</p>
|
|
<ul class="simple">
|
|
<li><ol class="first loweralpha">
|
|
<li>Use your browser to view an animated GIF movie.</li>
|
|
</ol>
|
|
</li>
|
|
</ul>
|
|
<p>Select “Open File” under the File menu
|
|
Load the animated GIF file</p>
|
|
<ul class="simple">
|
|
<li>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.</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>% mplayer foo.mpg
|
|
% ffplay bar.avi
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>c) Use the <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a>
|
|
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
|
|
which works directly on a series of image files.</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s">"foo*.jpg"</span><span class="p">)</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>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.</li>
|
|
</ul>
|
|
<hr class="docutils" />
|
|
<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></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>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>To write JPEG 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.</p>
|
|
<p>To write <em>movie</em> 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. Typically it’s name is lowercase,
|
|
i.e. ffmpeg.</p>
|
|
<p>See the <a class="reference internal" href="Section_start.html#start-2-4"><span>Making LAMMPS</span></a> section of the
|
|
documentation for details on how to compile with optional switches.</p>
|
|
<p>Note that since FFmpeg is run as an external program via a pipe,
|
|
LAMMPS has limited control over its execution and no knowledge about
|
|
errors and warnings printed by it. Those warnings and error messages
|
|
will be printed to the screen only. Due to the way image data is
|
|
communicated to FFmpeg, it will often print the message</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>pipe:: Input/output error
|
|
</pre></div>
|
|
</div>
|
|
<p>which can be safely ignored. Other warnings
|
|
and errors have to be addressed according to the FFmpeg documentation.
|
|
One known issue is that certain movie file formats (e.g. MPEG level 1
|
|
and 2 format streams) have video bandwith limits that can be crossed
|
|
when rendering too large of image sizes. Typical warnings look like
|
|
this:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>[mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it
|
|
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
|
|
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
|
|
</pre></div>
|
|
</div>
|
|
<p>In this case it is recommended to either reduce the size of the image
|
|
or encode in a different format that is also supported by your copy of
|
|
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
|
|
mp4).</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The defaults for the keywords are as follows:</p>
|
|
<ul class="simple">
|
|
<li>adiam = not specified (use diameter setting)</li>
|
|
<li>atom = yes</li>
|
|
<li>bond = none none (if no bonds in system)</li>
|
|
<li>bond = atom 0.5 (if bonds in system)</li>
|
|
<li>size = 512 512</li>
|
|
<li>view = 60 30 (for 3d)</li>
|
|
<li>view = 0 0 (for 2d)</li>
|
|
<li>center = s 0.5 0.5 0.5</li>
|
|
<li>up = 0 0 1 (for 3d)</li>
|
|
<li>up = 0 1 0 (for 2d)</li>
|
|
<li>zoom = 1.0</li>
|
|
<li>persp = 0.0</li>
|
|
<li>box = yes 0.02</li>
|
|
<li>axes = no 0.0 0.0</li>
|
|
<li>subbox no 0.0</li>
|
|
<li>shiny = 1.0</li>
|
|
<li>ssao = no</li>
|
|
</ul>
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