Description
Dump a high-quality rendered image of the atom configuration every N
timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as
well as the dump_modify command control what is
included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
below. Other dump styles store snapshots of numerical data asociated
with atoms in various formats, as discussed on the dump
doc page.
Note that a set of images or a movie can be made after a simulation
has been run, using the rerun command to read snapshots
from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie.
Here are two sample images, rendered as 1024x1024 JPEG files. Click
to see the full-size images:
Only atoms in the specified group are rendered in the image. The
dump_modify region and thresh commands can also
alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the image dump style. If the suffix is ”.jpg” or
”.jpeg”, then a JPEG format file is created, if the suffix is ”.png”,
then a PNG format is created, else a PPM (aka NETPBM) format file is
created. The JPEG and PNG files are binary; PPM has a text mode
header followed by binary data. JPEG images have lossy compression;
PNG has lossless compression; and PPM files are uncompressed but can
be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ”.gz” suffix is used.
Similarly, the format of the resulting movie is chosen with the
movie dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the dump_modify command.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
flag. See this section of the manual
for instructions on how to do this.
Note
Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
in the image may be slightly outside the simulation box.
Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the dump_modify first command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the dump_modify every command.
Dump image filenames must contain a wildcard character “*”, so that
one image file per snapshot is written. The “*” character is replaced
with the timestep value. For example, tmp.dump.*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the dump_modify pad command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.
Dump movie filenames on the other hand, must not have any wildcard
character since only one file combining all images into a single
movie will be written by the movie encoder.
The color and diameter settings determine the color and size of
atoms rendered in the image. They can be any atom attribute defined
for the dump custom command, including type and
element. This includes per-atom quantities calculated by a
compute, fix, or variable,
which are prefixed by “c_”, “f_”, or “v_” respectively. Note that the
diameter setting can be overridden with a numeric value applied to
all atoms by the optional adiam keyword.
If type is specified for the color setting, then the color of each
atom is determined by its atom type. By default the mapping of types
to colors is as follows:
- type 1 = red
- type 2 = green
- type 3 = blue
- type 4 = yellow
- type 5 = aqua
- type 6 = cyan
and repeats itself for types > 6. This mapping can be changed by the
dump_modify acolor command.
If type is specified for the diameter setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the dump_modify adiam command.
If element is specified for the color and/or diameter setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the “dump_modify element” command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the AtomEye visualization package.
If other atom attributes are used for the color or diameter
settings, they are interpreted in the following way.
If “vx”, for example, is used as the color setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a “color map”, which can be specified via the
dump_modify command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between “red” and “blue”, or
discretely so that the value of -3.2 is “orange”.
If “vx”, for example, is used as the diameter setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
atom_style sphere define a per-particle radius or
diameter, which can be used as the diameter setting.
The various kewords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The dump modify
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
The atom keyword allow you to turn off the drawing of all atoms, if
the specified value is no. Note that this will not turn off the
drawing of particles that are represented as lines, triangles, or
bodies, as discussed below. These particles can be drawn separately
if the line, tri, or body keywords are used.
The adiam keyword allows you to override the diameter setting to
set a single numeric size. All atoms will be drawn with that
-diameter, e.g. 1.5, which is in whatever distance units
+diameter, e.g. 1.5, which is in whatever distance units
the input script defines, e.g. Angstroms.
The bond 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
dump_modify command). By default, bonds are drawn
if they are defined in the input data file as read by the
read_data command. Using none for both the bond
color and width value will turn off the drawing of all bonds.
If atom is specified for the bond color 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.
If type is specified for the color 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:
- type 1 = red
- type 2 = green
- type 3 = blue
- type 4 = yellow
- type 5 = aqua
- type 6 = cyan
and repeats itself for bond types > 6. This mapping can be changed by
the dump_modify bcolor command.
The bond width value can be a numeric value or atom or type (or
none as indicated above).
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
-units the input script defines, e.g. Angstroms.
+
units the input script defines, e.g. Angstroms.
If atom is specified for the width value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.
If type is specified for the width 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 dump_modify bdiam command.
The line keyword can be used when atom_style line
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 color value is type, which will color
the lines according to the atom type of the particle. By default the
mapping of types to colors is as follows:
- type 1 = red
- type 2 = green
- type 3 = blue
- type 4 = yellow
- type 5 = aqua
- type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the dump_modify command.
The line width 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 units the input script defines,
+is in whatever distance units the input script defines,
e.g. Angstroms.
The tri keyword can be used when atom_style tri is
used to define particles as triangles, and will draw them as triangles
or edges (3 lines) or both, depending on the setting for tflag. If
edges are drawn, the width 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 color value is type, which will
color the triangles according to the atom type of the particle. By
default the mapping of types to colors is as follows:
- type 1 = red
- type 2 = green
- type 3 = blue
- type 4 = yellow
- type 5 = aqua
- type 6 = cyan
and repeats itself for types > 6. There is not yet an option to
change this via the dump_modify command.
The body keyword can be used when atom_style body
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.
The body 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 bflag1 and bflag2 settings are numerical values which are
passed to the body style to affect how the drawing of a body particle
is done. See the body doc page for a description of what
these parameters mean for each body style.
The size keyword sets the width and height of the created images,
i.e. the number of pixels in each direction.
The view, center, up, zoom, and persp 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.
All of the view, center, up, zoom, and persp values can be
specified as numeric quantities, whose meaning is explained below.
Any of them can also be specified as an equal-style variable, 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.
The view keyword determines the viewpoint from which the simulation
box is viewed, looking towards the center point. The theta value
is the vertical angle from the +z axis, and must be an angle from 0 to
180 degrees. The phi 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 center point. If theta or phi are
specified via variables, then the variable values should be in
degrees.
The center keyword determines the point in simulation space that
will be at the center of the image. Cx, Cy, and Cz 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 Cx, Cy, or Cz you may get a blank image. Internally,
Cx, Cy, and Cz are converted into a point in simulation space.
If flag is set to “s” for static, then this conversion is done once,
at the time the dump command is issued. If flag 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.
The up 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 theta and
pni 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 up vector as
up_internal = view cross (up cross view)
This means the only restriction on the specified up vector is that
it cannot be parallel to the view vector, implied by the theta and
phi values.
The zoom keyword scales the size of the simulation box as it appears
in the image. The default zfactor value of 1 should display an
image mostly filled by the atoms in the simulation box. A zfactor >
1 will make the simulation box larger; a zfactor < 1 will make it
smaller. Zfactor must be a value > 0.0.
The persp 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 pfactor value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A pfactor
value between 0.0 and 1.0 will introduce more perspective. A pfactor
value > 1 will create a highly skewed image with a large amount of
perspective.
Note
The persp keyword is not yet supported as an option.
The box keyword determines if and how the simulation box boundaries
are rendered as thin cylinders in the image. If no is set, then the
box boundaries are not drawn and the diam setting is ignored. If
yes 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 dump_modify boxcolor command.
The axes keyword determines if and how the coordinate axes are
rendered as thin cylinders in the image. If no is set, then the
axes are not drawn and the length and diam settings are ignored.
If yes 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 length
setting determines how long the cylinders will be as a fraction of the
respective box lengths. The diam setting determines their thickness
as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d).
The subbox keyword determines if and how processor sub-domain
boundaries are rendered as thin cylinders in the image. If no is
set (default), then the sub-domain boundaries are not drawn and the
diam setting is ignored. If yes 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 dump_modify boxcolor command.
The shiny keyword determines how shiny the objects rendered in the
image will appear. The sfactor value must be a value 0.0 <=
sfactor <= 1.0, where sfactor = 1 is a highly reflective surface
and sfactor = 0 is a rough non-shiny surface.
The ssao keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If yes 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 dfactor parameter. If no is set, no depth
shading is performed.
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 movie 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.
To manually convert JPEG, PNG or PPM files into an animated GIF or
MPEG or other movie file you can use:
- Use the ImageMagick convert program.
% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg
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.
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. 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.
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
Frontends for FFmpeg exist for multiple platforms. For more
information see the FFmpeg homepage
Play the movie:
- Use your browser to view an animated GIF movie.
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.
% mplayer foo.mpg
% ffplay bar.avi
- 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.
See Section_modify 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.
