Merge pull request #3015 from lammps/dump-image-doc
Move dump_modify options specific to image/movie to dump image doc page
This commit is contained in:
Axel Kohlmeyer
@ -6,6 +6,8 @@ dump image command
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dump movie command
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==================
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(see below for :ref:`dump_modify options <dump_modify_image>` specific to dump image/movie)
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Syntax
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""""""
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@ -15,7 +17,7 @@ Syntax
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* ID = user-assigned name for the dump
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* group-ID = ID of the group of atoms to be imaged
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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 :doc:`dump <dump>` doc page)
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* style = *image* or *movie* = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
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* N = dump every this many timesteps
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* file = name of file to write image to
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* color = atom attribute that determines color of each atom
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@ -79,6 +81,69 @@ Syntax
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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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.. _dump_modify_image:
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dump_modify options for dump image/movie
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========================================
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Syntax
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""""""
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.. parsed-literal::
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dump_modify dump-ID keyword values ...
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* these keywords apply only to the *image* and *movie* styles and are documented on this page
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* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
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* see the :doc:`dump modify <dump_modify>` doc page for more general keywords
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.. parsed-literal::
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*acolor* args = type color
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type = atom type or range of types (see below)
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color = name of color or color1/color2/...
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*adiam* args = type diam
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type = atom type or range of types (see below)
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diam = diameter of atoms of that type (distance units)
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*amap* args = lo hi style delta N entry1 entry2 ... entryN
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lo = number or *min* = lower bound of range of color map
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hi = number or *max* = upper bound of range of color map
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style = 2 letters = "c" or "d" or "s" plus "a" or "f"
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"c" for continuous
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"d" for discrete
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"s" for sequential
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"a" for absolute
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"f" for fractional
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delta = binsize (only used for style "s", otherwise ignored)
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binsize = range is divided into bins of this width
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N = # of subsequent entries
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entry = value color (for continuous style)
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value = number or *min* or *max* = single value within range
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color = name of color used for that value
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entry = lo hi color (for discrete style)
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lo/hi = number or *min* or *max* = lower/upper bound of subset of range
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color = name of color used for that subset of values
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entry = color (for sequential style)
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color = name of color used for a bin of values
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*backcolor* arg = color
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color = name of color for background
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*bcolor* args = type color
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type = bond type or range of types (see below)
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color = name of color or color1/color2/...
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*bdiam* args = type diam
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type = bond type or range of types (see below)
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diam = diameter of bonds of that type (distance units)
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*boxcolor* arg = color
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color = name of color for simulation box lines and processor sub-domain lines
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*color* args = name R G B
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name = name of color
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R,G,B = red/green/blue numeric values from 0.0 to 1.0
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*bitrate* arg = rate
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rate = target bitrate for movie in kbps
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*framerate* arg = fps
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fps = frames per second for movie
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Examples
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""""""""
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@ -91,6 +156,8 @@ Examples
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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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dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
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Description
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"""""""""""
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@ -145,10 +212,10 @@ 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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<http://ffmpeg.org/ffmpeg.html>`_.
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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 :doc:`dump_modify <dump_modify>` command.
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<http://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
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.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
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compression like bitrate and framerate can be set using the
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dump_modify command as described below.
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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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@ -210,19 +277,20 @@ to colors is as follows:
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* type 6 = cyan
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and repeats itself for types > 6. This mapping can be changed by the
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:doc:`dump_modify acolor <dump_modify>` command.
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"dump_modify acolor" command, as described below.
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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 :doc:`dump_modify adiam <dump_modify>` command.
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diameter 1.0. This mapping can be changed by the "dump_modify adiam"
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command, as described below.
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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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mapping specified by the "dump_modify element" command, as described
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below. By default every atom type is C (carbon). Every element has a
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color and diameter associated with it, which is the same as the colors
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and sizes used by the `AtomEye <atomeye_>`_ visualization package.
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.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
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@ -232,13 +300,13 @@ 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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:doc:`dump_modify <dump_modify>` 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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a "color map", which can be specified via the dump_modify command, as
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described below. The basic idea is that the atom-attribute will be
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within a range of values, and every value within the range is mapped
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to a specific color. Depending on how the color map is defined, that
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mapping can take place via interpolation so that a value of -3.2 is
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halfway between "red" and "blue", or discretely so that the value of
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-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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@ -251,9 +319,10 @@ diameter, which can be used as the *diameter* setting.
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The various keywords 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 :doc:`dump modify <dump_modify>`
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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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will likely not need to change. As described below, the dump modify
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command also has options specific to the dump image style,
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particularly for assigning colors to atoms, bonds, and other image
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features.
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----------
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@ -295,7 +364,7 @@ types to colors is as follows:
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* type 6 = cyan
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and repeats itself for bond types > 6. This mapping can be changed by
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the :doc:`dump_modify bcolor <dump_modify>` command.
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the "dump_modify bcolor" command, as described below.
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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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@ -310,7 +379,8 @@ 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 :doc:`dump_modify bdiam <dump_modify>` command.
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diameter 0.5. This mapping can be changed by the "dump_modify bdiam" command,
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as described below.
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----------
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@ -330,7 +400,7 @@ mapping of types to colors is as follows:
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* type 6 = cyan
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and repeats itself for types > 6. There is not yet an option to
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change this via the :doc:`dump_modify <dump_modify>` command.
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change this via the dump_modify command.
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The line *width* can only be a numeric value, which specifies that all
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lines will be drawn as cylinders with that diameter, e.g. 1.0, which
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@ -357,7 +427,7 @@ default the mapping of types to colors is as follows:
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* type 6 = cyan
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and repeats itself for types > 6. There is not yet an option to
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change this via the :doc:`dump_modify <dump_modify>` command.
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change this via the dump_modify command.
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----------
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@ -390,7 +460,7 @@ particle. By default the mapping of types to colors is as follows:
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* type 6 = cyan
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and repeats itself for types > 6. There is not yet an option to
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change this via the :doc:`dump_modify <dump_modify>` command.
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change this via the dump_modify command.
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----------
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@ -414,7 +484,7 @@ the mapping of types to colors is as follows:
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* type 6 = cyan
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and repeats itself for types > 6. There is not yet an option to
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change this via the :doc:`dump_modify <dump_modify>` command.
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change this via the dump_modify command.
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----------
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@ -488,7 +558,8 @@ are rendered as thin cylinders in the image. If *no* is set, then the
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box boundaries are not drawn and the *diam* setting is ignored. If
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*yes* is set, the 12 edges of the box are drawn, with a diameter that
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is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
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2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
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2d). The color of the box boundaries can be set with the "dump_modify
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boxcolor" command.
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The *axes* keyword determines if and how the coordinate axes are
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rendered as thin cylinders in the image. If *no* is set, then the
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@ -507,7 +578,8 @@ set (default), then the sub-domain boundaries are not drawn and the
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*diam* setting is ignored. If *yes* is set, the 12 edges of each
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processor sub-domain are drawn, with a diameter that is a fraction of
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the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
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of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
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of the sub-domain boundaries can be set with the "dump_modify
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boxcolor" command.
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----------
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@ -607,9 +679,272 @@ Play the movie:
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----------
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See the :doc:`Modify <Modify>` page for information on how to add
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new compute and fix styles to LAMMPS to calculate per-atom quantities
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which could then be output into dump files.
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Dump_modify keywords for dump image and dump movie
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""""""""""""""""""""""""""""""""""""""""""""""""""
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The following dump_modify keywords apply only to the dump image and
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dump movie styles. Any keyword that works with dump image also works
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with dump movie, since the movie is simply a collection of images.
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Some of the keywords only affect the dump movie style. The
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descriptions give details.
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----------
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The *acolor* keyword can be used with the dump image command, when its
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atom color setting is *type*, to set the color that atoms of each type
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will be drawn in the image.
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The specified *type* should be an integer from 1 to Ntypes = the
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number of atom types. A wildcard asterisk can be used in place of or
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in conjunction with the *type* argument to specify a range of atom
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types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
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the number of atom types, then an asterisk with no numeric values
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means all types from 1 to N. A leading asterisk means all types from
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1 to n (inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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The specified *color* can be a single color which is any of the 140
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pre-defined colors (see below) or a color name defined by the
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"dump_modify color" command, as described below. Or it can be two or
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more colors separated by a "/" character, e.g. red/green/blue. In the
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former case, that color is assigned to all the specified atom types.
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In the latter case, the list of colors are assigned in a round-robin
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fashion to each of the specified atom types.
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----------
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The *adiam* keyword can be used with the dump image command, when its
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atom diameter setting is *type*, to set the size that atoms of each
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type will be drawn in the image. The specified *type* should be an
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integer from 1 to Ntypes. As with the *acolor* keyword, a wildcard
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asterisk can be used as part of the *type* argument to specify a range
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of atom types. The specified *diam* is the size in whatever distance
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:doc:`units <units>` the input script is using, e.g. Angstroms.
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----------
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The *amap* keyword can be used with the dump image command, with its
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*atom* keyword, when its atom setting is an atom-attribute, to setup a
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color map. The color map is used to assign a specific RGB
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(red/green/blue) color value to an individual atom when it is drawn,
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based on the atom's attribute, which is a numeric value, e.g. its
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x-component of velocity if the atom-attribute "vx" was specified.
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The basic idea of a color map is that the atom-attribute will be
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within a range of values, and that range is associated with a series
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of colors (e.g. red, blue, green). An atom's specific value (vx =
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-3.2) can then mapped to the series of colors (e.g. halfway between
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red and blue), and a specific color is determined via an interpolation
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procedure.
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There are many possible options for the color map, enabled by the
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*amap* keyword. Here are the details.
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The *lo* and *hi* settings determine the range of values allowed for
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the atom attribute. If numeric values are used for *lo* and/or *hi*,
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then values that are lower/higher than that value are set to the
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value. I.e. the range is static. If *lo* is specified as *min* or
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*hi* as *max* then the range is dynamic, and the lower and/or
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upper bound will be calculated each time an image is drawn, based
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on the set of atoms being visualized.
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The *style* setting is two letters, such as "ca". The first letter is
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either "c" for continuous, "d" for discrete, or "s" for sequential.
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The second letter is either "a" for absolute, or "f" for fractional.
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A continuous color map is one in which the color changes continuously
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from value to value within the range. A discrete color map is one in
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which discrete colors are assigned to sub-ranges of values within the
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range. A sequential color map is one in which discrete colors are
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assigned to a sequence of sub-ranges of values covering the entire
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range.
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An absolute color map is one in which the values to which colors are
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assigned are specified explicitly as values within the range. A
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fractional color map is one in which the values to which colors are
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assigned are specified as a fractional portion of the range. For
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example if the range is from -10.0 to 10.0, and the color red is to be
|
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assigned to atoms with a value of 5.0, then for an absolute color map
|
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the number 5.0 would be used. But for a fractional map, the number
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0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
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The *delta* setting must be specified for all styles, but is only used
|
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for the sequential style; otherwise the value is ignored. It
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specifies the bin size to use within the range for assigning
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consecutive colors to. For example, if the range is from -10.0 to
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10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
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the range. The first will be from -10.0 <= color1 < -9.0, then second
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from -9.0 <= color2 < -8.0, etc.
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The *N* setting is how many entries follow. The format of the entries
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depends on whether the color map style is continuous, discrete or
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sequential. In all cases the *color* setting can be any of the 140
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pre-defined colors (see below) or a color name defined by the
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dump_modify color option.
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For continuous color maps, each entry has a *value* and a *color*\ .
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The *value* is either a number within the range of values or *min* or
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*max*\ . The *value* of the first entry must be *min* and the *value*
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of the last entry must be *max*\ . Any entries in between must have
|
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increasing values. Note that numeric values can be specified either
|
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as absolute numbers or as fractions (0.0 to 1.0) of the range,
|
||||
depending on the "a" or "f" in the style setting for the color map.
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||||
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||||
Here is how the entries are used to determine the color of an
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individual atom, given the value X of its atom attribute. X will fall
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between 2 of the entry values. The color of the atom is linearly
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interpolated (in each of the RGB values) between the 2 colors
|
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associated with those entries. For example, if X = -5.0 and the 2
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surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
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atom's color will be halfway between "red" and "blue", which happens
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to be "purple".
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For discrete color maps, each entry has a *lo* and *hi* value and a
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*color*\ . The *lo* and *hi* settings are either numbers within the
|
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range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
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||||
and *hi* settings of the last entry must be *min* and *max*\ . Other
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entries can have any *lo* and *hi* values and the sub-ranges of
|
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different values can overlap. Note that numeric *lo* and *hi* values
|
||||
can be specified either as absolute numbers or as fractions (0.0 to
|
||||
1.0) of the range, depending on the "a" or "f" in the style setting
|
||||
for the color map.
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||||
|
||||
Here is how the entries are used to determine the color of an
|
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individual atom, given the value X of its atom attribute. The entries
|
||||
are scanned from first to last. The first time that *lo* <= X <=
|
||||
*hi*, X is assigned the color associated with that entry. You can
|
||||
think of the last entry as assigning a default color (since it will
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always be matched by X), and the earlier entries as colors that
|
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override the default. Also note that no interpolation of a color RGB
|
||||
is done. All atoms will be drawn with one of the colors in the list
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of entries.
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||||
|
||||
For sequential color maps, each entry has only a *color*\ . Here is how
|
||||
the entries are used to determine the color of an individual atom,
|
||||
given the value X of its atom attribute. The range is partitioned
|
||||
into N bins of width *binsize*\ . Thus X will fall in a specific bin
|
||||
from 1 to N, say the Mth bin. If it falls on a boundary between 2
|
||||
bins, it is considered to be in the higher of the 2 bins. Each bin is
|
||||
assigned a color from the E entries. If E < N, then the colors are
|
||||
repeated. For example if 2 entries with colors red and green are
|
||||
specified, then the odd numbered bins will be red and the even bins
|
||||
green. The color of the atom is the color of its bin. Note that the
|
||||
sequential color map is really a shorthand way of defining a discrete
|
||||
color map without having to specify where all the bin boundaries are.
|
||||
|
||||
Here is an example of using a sequential color map to color all the
|
||||
atoms in individual molecules with a different color. See the
|
||||
examples/pour/in.pour.2d.molecule input script for an example of how
|
||||
this is used.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
variable colors string &
|
||||
"red green blue yellow white &
|
||||
purple pink orange lime gray"
|
||||
variable mol atom mol%10
|
||||
dump 1 all image 250 image.*.jpg v_mol type &
|
||||
zoom 1.6 adiam 1.5
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
In this case, 10 colors are defined, and molecule IDs are
|
||||
mapped to one of the colors, even if there are 1000s of molecules.
|
||||
|
||||
----------
|
||||
|
||||
The *backcolor* sets the background color of the images. The color
|
||||
name can be any of the 140 pre-defined colors (see below) or a color
|
||||
name defined by the dump_modify color option.
|
||||
|
||||
----------
|
||||
|
||||
The *bcolor* keyword can be used with the dump image command, with its
|
||||
*bond* keyword, when its color setting is *type*, to set the color
|
||||
that bonds of each type will be drawn in the image.
|
||||
|
||||
The specified *type* should be an integer from 1 to Nbondtypes = the
|
||||
number of bond types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the *type* argument to specify a range of bond
|
||||
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
|
||||
the number of bond types, then an asterisk with no numeric values
|
||||
means all types from 1 to N. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
The specified *color* can be a single color which is any of the 140
|
||||
pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option. Or it can be two or more colors separated
|
||||
by a "/" character, e.g. red/green/blue. In the former case, that
|
||||
color is assigned to all the specified bond types. In the latter
|
||||
case, the list of colors are assigned in a round-robin fashion to each
|
||||
of the specified bond types.
|
||||
|
||||
----------
|
||||
|
||||
The *bdiam* keyword can be used with the dump image command, with its
|
||||
*bond* keyword, when its diam setting is *type*, to set the diameter
|
||||
that bonds of each type will be drawn in the image. The specified
|
||||
*type* should be an integer from 1 to Nbondtypes. As with the
|
||||
*bcolor* keyword, a wildcard asterisk can be used as part of the
|
||||
*type* argument to specify a range of bond types. The specified
|
||||
*diam* is the size in whatever distance :doc:`units <units>` you are
|
||||
using, e.g. Angstroms.
|
||||
|
||||
----------
|
||||
|
||||
The *bitrate* keyword can be used with the :doc:`dump movie
|
||||
<dump_image>` command to define the size of the resulting movie file
|
||||
and its quality via setting how many kbits per second are to be used
|
||||
for the movie file. Higher bitrates require less compression and will
|
||||
result in higher quality movies. The quality is also determined by
|
||||
the compression format and encoder. The default setting is 2000
|
||||
kbit/s, which will result in average quality with older compression
|
||||
formats.
|
||||
|
||||
.. note::
|
||||
|
||||
Not all movie file formats supported by dump movie allow the
|
||||
bitrate to be set. If not, the setting is silently ignored.
|
||||
|
||||
----------
|
||||
|
||||
The *boxcolor* keyword sets the color of the simulation box drawn
|
||||
around the atoms in each image as well as the color of processor
|
||||
sub-domain boundaries. See the "dump image box" command for how to
|
||||
specify that a box be drawn via the *box* keyword, and the sub-domain
|
||||
boundaries via the *subbox* keyword. The color name can be any of the
|
||||
140 pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option.
|
||||
|
||||
----------
|
||||
|
||||
The *color* keyword allows definition of a new color name, in addition
|
||||
to the 140-predefined colors (see below), and associates 3
|
||||
red/green/blue RGB values with that color name. The color name can
|
||||
then be used with any other dump_modify keyword that takes a color
|
||||
name as a value. The RGB values should each be floating point values
|
||||
between 0.0 and 1.0 inclusive.
|
||||
|
||||
When a color name is converted to RGB values, the user-defined color
|
||||
names are searched first, then the 140 pre-defined color names. This
|
||||
means you can also use the *color* keyword to overwrite one of the
|
||||
pre-defined color names with new RBG values.
|
||||
|
||||
----------
|
||||
|
||||
The *framerate* keyword can be used with the :doc:`dump movie
|
||||
<dump_image>` command to define the duration of the resulting movie
|
||||
file. Movie files written by the dump *movie* command have a default
|
||||
frame rate of 24 frames per second and the images generated will be
|
||||
converted at that rate. Thus a sequence of 1000 dump images will
|
||||
result in a movie of about 42 seconds. To make a movie run longer you
|
||||
can either generate images more frequently or lower the frame rate.
|
||||
To speed a movie up, you can do the inverse. Using a frame rate
|
||||
higher than 24 is not recommended, as it will result in simply
|
||||
dropping the rendered images. It is more efficient to dump images less
|
||||
frequently.
|
||||
|
||||
----------
|
||||
|
||||
@ -664,7 +999,7 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The defaults for the keywords are as follows:
|
||||
The defaults for the dump image and dump movie keywords are as follows:
|
||||
|
||||
* adiam = not specified (use diameter setting)
|
||||
* atom = yes
|
||||
@ -682,3 +1017,101 @@ The defaults for the keywords are as follows:
|
||||
* subbox no 0.0
|
||||
* shiny = 1.0
|
||||
* ssao = no
|
||||
|
||||
----------
|
||||
|
||||
The defaults for the dump_modify keywords specific to dump image and dump movie are as follows:
|
||||
|
||||
* acolor = \* red/green/blue/yellow/aqua/cyan
|
||||
* adiam = \* 1.0
|
||||
* amap = min max cf 0.0 2 min blue max red
|
||||
* backcolor = black
|
||||
* bcolor = \* red/green/blue/yellow/aqua/cyan
|
||||
* bdiam = \* 0.5
|
||||
* bitrate = 2000
|
||||
* boxcolor = yellow
|
||||
* color = 140 color names are pre-defined as listed below
|
||||
* framerate = 24
|
||||
|
||||
----------
|
||||
|
||||
These are the standard 109 element names that LAMMPS pre-defines for
|
||||
use with the dump image and dump_modify commands.
|
||||
|
||||
* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
|
||||
* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
|
||||
* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
|
||||
* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
|
||||
* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
|
||||
* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
|
||||
* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
|
||||
* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
|
||||
* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
|
||||
* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
|
||||
* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
|
||||
|
||||
----------
|
||||
|
||||
These are the 140 colors that LAMMPS pre-defines for use with the dump
|
||||
image and dump_modify commands. Additional colors can be defined with
|
||||
the dump_modify color command. The 3 numbers listed for each name are
|
||||
the RGB (red/green/blue) values. Divide each value by 255 to get the
|
||||
equivalent 0.0 to 1.0 value.
|
||||
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
|
||||
@ -3,6 +3,9 @@
|
||||
dump_modify command
|
||||
===================
|
||||
|
||||
:doc:`dump_modify <dump_image>` command for image/movie options
|
||||
===============================================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -12,8 +15,9 @@ Syntax
|
||||
|
||||
* dump-ID = ID of dump to modify
|
||||
* one or more keyword/value pairs may be appended
|
||||
|
||||
* these keywords apply to various dump styles
|
||||
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
||||
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -35,6 +39,9 @@ Syntax
|
||||
*format* args = *line* string, *int* string, *float* string, M string, or *none*
|
||||
string = C-style format string
|
||||
M = integer from 1 to N, where N = # of per-atom quantities being output
|
||||
*header* arg = *yes* or *no*
|
||||
*yes* to write the header
|
||||
*no* to not write the header
|
||||
*image* arg = *yes* or *no*
|
||||
*label* arg = string
|
||||
string = character string (e.g. BONDS) to use in header of dump local file
|
||||
@ -66,56 +73,11 @@ Syntax
|
||||
*unwrap* arg = *yes* or *no*
|
||||
|
||||
* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
|
||||
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
|
||||
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*acolor* args = type color
|
||||
type = atom type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
*adiam* args = type diam
|
||||
type = atom type or range of types (see below)
|
||||
diam = diameter of atoms of that type (distance units)
|
||||
*amap* args = lo hi style delta N entry1 entry2 ... entryN
|
||||
lo = number or *min* = lower bound of range of color map
|
||||
hi = number or *max* = upper bound of range of color map
|
||||
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
|
||||
"c" for continuous
|
||||
"d" for discrete
|
||||
"s" for sequential
|
||||
"a" for absolute
|
||||
"f" for fractional
|
||||
delta = binsize (only used for style "s", otherwise ignored)
|
||||
binsize = range is divided into bins of this width
|
||||
N = # of subsequent entries
|
||||
entry = value color (for continuous style)
|
||||
value = number or *min* or *max* = single value within range
|
||||
color = name of color used for that value
|
||||
entry = lo hi color (for discrete style)
|
||||
lo/hi = number or *min* or *max* = lower/upper bound of subset of range
|
||||
color = name of color used for that subset of values
|
||||
entry = color (for sequential style)
|
||||
color = name of color used for a bin of values
|
||||
*backcolor* arg = color
|
||||
color = name of color for background
|
||||
*bcolor* args = type color
|
||||
type = bond type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
*bdiam* args = type diam
|
||||
type = bond type or range of types (see below)
|
||||
diam = diameter of bonds of that type (distance units)
|
||||
*boxcolor* arg = color
|
||||
color = name of color for simulation box lines and processor sub-domain lines
|
||||
*color* args = name R G B
|
||||
name = name of color
|
||||
R,G,B = red/green/blue numeric values from 0.0 to 1.0
|
||||
*bitrate* arg = rate
|
||||
rate = target bitrate for movie in kbps
|
||||
*framerate* arg = fps
|
||||
fps = frames per second for movie
|
||||
*header* arg = *yes* or *no*
|
||||
*yes* to write the header
|
||||
*no* to not write the header
|
||||
see the :doc:`dump image <dump_image>` doc page for details
|
||||
|
||||
* these keywords apply only to the */gz* and */zstd* dump styles
|
||||
* keyword = *compression_level*
|
||||
@ -126,7 +88,7 @@ Syntax
|
||||
level = integer specifying the compression level that should be used (see below for supported levels)
|
||||
|
||||
* these keywords apply only to the */zstd* dump styles
|
||||
* keyword = *compression_level*
|
||||
* keyword = *checksum*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -144,7 +106,6 @@ Examples
|
||||
dump_modify xtcdump precision 10000 sfactor 0.1
|
||||
dump_modify 1 every 1000 nfile 20
|
||||
dump_modify 1 every v_myVar
|
||||
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -163,8 +124,9 @@ which allow for use of MPI-IO.
|
||||
|
||||
----------
|
||||
|
||||
These keywords apply to various dump styles, including the :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles. The
|
||||
description gives details.
|
||||
Unless otherwise noted, the following keywords apply to all the
|
||||
various dump styles, including the :doc:`dump image <dump_image>` and
|
||||
:doc:`dump movie <dump_image>` styles.
|
||||
|
||||
----------
|
||||
|
||||
@ -380,6 +342,13 @@ The *fileper* keyword is documented below with the *nfile* keyword.
|
||||
|
||||
----------
|
||||
|
||||
The *header* keyword toggles whether the dump file will include a header.
|
||||
Excluding a header will reduce the size of the dump file for fixes such as
|
||||
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
|
||||
typically written to the header.
|
||||
|
||||
----------
|
||||
|
||||
The *image* keyword applies only to the dump *atom* style. If the
|
||||
image value is *yes*, 3 flags are appended to each atom's coords which
|
||||
are the absolute box image of the atom in each dimension. For
|
||||
@ -715,297 +684,27 @@ box size stored with the snapshot.
|
||||
|
||||
----------
|
||||
|
||||
These keywords apply only to the :doc:`dump image <dump_image>` and
|
||||
:doc:`dump movie <dump_image>` styles. Any keyword that affects an
|
||||
image, also affects a movie, since the movie is simply a collection of
|
||||
images. Some of the keywords only affect the :doc:`dump movie <dump_image>` style. The descriptions give details.
|
||||
The COMPRESS package offers both GZ and Zstd compression variants of
|
||||
styles atom, custom, local, cfg, and xyz. When using these styles the
|
||||
compression level can be controlled by the :code:`compression_level`
|
||||
keyword. File names with these styles have to end in either
|
||||
:code:`.gz` or :code:`.zst`.
|
||||
|
||||
----------
|
||||
|
||||
The *acolor* keyword can be used with the :doc:`dump image <dump_image>`
|
||||
command, when its atom color setting is *type*, to set the color that
|
||||
atoms of each type will be drawn in the image.
|
||||
|
||||
The specified *type* should be an integer from 1 to Ntypes = the
|
||||
number of atom types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the *type* argument to specify a range of atom
|
||||
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
|
||||
number of atom types, then an asterisk with no numeric values means
|
||||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
The specified *color* can be a single color which is any of the 140
|
||||
pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option. Or it can be two or more colors separated
|
||||
by a "/" character, e.g. red/green/blue. In the former case, that
|
||||
color is assigned to all the specified atom types. In the latter
|
||||
case, the list of colors are assigned in a round-robin fashion to each
|
||||
of the specified atom types.
|
||||
|
||||
----------
|
||||
|
||||
The *adiam* keyword can be used with the :doc:`dump image <dump_image>`
|
||||
command, when its atom diameter setting is *type*, to set the size
|
||||
that atoms of each type will be drawn in the image. The specified
|
||||
*type* should be an integer from 1 to Ntypes. As with the *acolor*
|
||||
keyword, a wildcard asterisk can be used as part of the *type*
|
||||
argument to specify a range of atom types. The specified *diam* is
|
||||
the size in whatever distance :doc:`units <units>` the input script is
|
||||
using, e.g. Angstroms.
|
||||
|
||||
----------
|
||||
|
||||
The *amap* keyword can be used with the :doc:`dump image <dump_image>`
|
||||
command, with its *atom* keyword, when its atom setting is an
|
||||
atom-attribute, to setup a color map. The color map is used to assign
|
||||
a specific RGB (red/green/blue) color value to an individual atom when
|
||||
it is drawn, based on the atom's attribute, which is a numeric value,
|
||||
e.g. its x-component of velocity if the atom-attribute "vx" was
|
||||
specified.
|
||||
|
||||
The basic idea of a color map is that the atom-attribute will be
|
||||
within a range of values, and that range is associated with a series
|
||||
of colors (e.g. red, blue, green). An atom's specific value (vx =
|
||||
-3.2) can then mapped to the series of colors (e.g. halfway between
|
||||
red and blue), and a specific color is determined via an interpolation
|
||||
procedure.
|
||||
|
||||
There are many possible options for the color map, enabled by the
|
||||
*amap* keyword. Here are the details.
|
||||
|
||||
The *lo* and *hi* settings determine the range of values allowed for
|
||||
the atom attribute. If numeric values are used for *lo* and/or *hi*,
|
||||
then values that are lower/higher than that value are set to the
|
||||
value. I.e. the range is static. If *lo* is specified as *min* or
|
||||
*hi* as *max* then the range is dynamic, and the lower and/or
|
||||
upper bound will be calculated each time an image is drawn, based
|
||||
on the set of atoms being visualized.
|
||||
|
||||
The *style* setting is two letters, such as "ca". The first letter is
|
||||
either "c" for continuous, "d" for discrete, or "s" for sequential.
|
||||
The second letter is either "a" for absolute, or "f" for fractional.
|
||||
|
||||
A continuous color map is one in which the color changes continuously
|
||||
from value to value within the range. A discrete color map is one in
|
||||
which discrete colors are assigned to sub-ranges of values within the
|
||||
range. A sequential color map is one in which discrete colors are
|
||||
assigned to a sequence of sub-ranges of values covering the entire
|
||||
range.
|
||||
|
||||
An absolute color map is one in which the values to which colors are
|
||||
assigned are specified explicitly as values within the range. A
|
||||
fractional color map is one in which the values to which colors are
|
||||
assigned are specified as a fractional portion of the range. For
|
||||
example if the range is from -10.0 to 10.0, and the color red is to be
|
||||
assigned to atoms with a value of 5.0, then for an absolute color map
|
||||
the number 5.0 would be used. But for a fractional map, the number
|
||||
0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
|
||||
|
||||
The *delta* setting must be specified for all styles, but is only used
|
||||
for the sequential style; otherwise the value is ignored. It
|
||||
specifies the bin size to use within the range for assigning
|
||||
consecutive colors to. For example, if the range is from -10.0 to
|
||||
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
|
||||
the range. The first will be from -10.0 <= color1 < -9.0, then second
|
||||
from -9.0 <= color2 < -8.0, etc.
|
||||
|
||||
The *N* setting is how many entries follow. The format of the entries
|
||||
depends on whether the color map style is continuous, discrete or
|
||||
sequential. In all cases the *color* setting can be any of the 140
|
||||
pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option.
|
||||
|
||||
For continuous color maps, each entry has a *value* and a *color*\ .
|
||||
The *value* is either a number within the range of values or *min* or
|
||||
*max*\ . The *value* of the first entry must be *min* and the *value*
|
||||
of the last entry must be *max*\ . Any entries in between must have
|
||||
increasing values. Note that numeric values can be specified either
|
||||
as absolute numbers or as fractions (0.0 to 1.0) of the range,
|
||||
depending on the "a" or "f" in the style setting for the color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value X of its atom attribute. X will fall
|
||||
between 2 of the entry values. The color of the atom is linearly
|
||||
interpolated (in each of the RGB values) between the 2 colors
|
||||
associated with those entries. For example, if X = -5.0 and the 2
|
||||
surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
|
||||
atom's color will be halfway between "red" and "blue", which happens
|
||||
to be "purple".
|
||||
|
||||
For discrete color maps, each entry has a *lo* and *hi* value and a
|
||||
*color*\ . The *lo* and *hi* settings are either numbers within the
|
||||
range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
|
||||
and *hi* settings of the last entry must be *min* and *max*\ . Other
|
||||
entries can have any *lo* and *hi* values and the sub-ranges of
|
||||
different values can overlap. Note that numeric *lo* and *hi* values
|
||||
can be specified either as absolute numbers or as fractions (0.0 to
|
||||
1.0) of the range, depending on the "a" or "f" in the style setting
|
||||
for the color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value X of its atom attribute. The entries
|
||||
are scanned from first to last. The first time that *lo* <= X <=
|
||||
*hi*, X is assigned the color associated with that entry. You can
|
||||
think of the last entry as assigning a default color (since it will
|
||||
always be matched by X), and the earlier entries as colors that
|
||||
override the default. Also note that no interpolation of a color RGB
|
||||
is done. All atoms will be drawn with one of the colors in the list
|
||||
of entries.
|
||||
|
||||
For sequential color maps, each entry has only a *color*\ . Here is how
|
||||
the entries are used to determine the color of an individual atom,
|
||||
given the value X of its atom attribute. The range is partitioned
|
||||
into N bins of width *binsize*\ . Thus X will fall in a specific bin
|
||||
from 1 to N, say the Mth bin. If it falls on a boundary between 2
|
||||
bins, it is considered to be in the higher of the 2 bins. Each bin is
|
||||
assigned a color from the E entries. If E < N, then the colors are
|
||||
repeated. For example if 2 entries with colors red and green are
|
||||
specified, then the odd numbered bins will be red and the even bins
|
||||
green. The color of the atom is the color of its bin. Note that the
|
||||
sequential color map is really a shorthand way of defining a discrete
|
||||
color map without having to specify where all the bin boundaries are.
|
||||
|
||||
Here is an example of using a sequential color map to color all the
|
||||
atoms in individual molecules with a different color. See the
|
||||
examples/pour/in.pour.2d.molecule input script for an example of how
|
||||
this is used.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
variable colors string &
|
||||
"red green blue yellow white &
|
||||
purple pink orange lime gray"
|
||||
variable mol atom mol%10
|
||||
dump 1 all image 250 image.*.jpg v_mol type &
|
||||
zoom 1.6 adiam 1.5
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
In this case, 10 colors are defined, and molecule IDs are
|
||||
mapped to one of the colors, even if there are 1000s of molecules.
|
||||
|
||||
----------
|
||||
|
||||
The *backcolor* sets the background color of the images. The color
|
||||
name can be any of the 140 pre-defined colors (see below) or a color
|
||||
name defined by the dump_modify color option.
|
||||
|
||||
----------
|
||||
|
||||
The *bcolor* keyword can be used with the :doc:`dump image <dump_image>`
|
||||
command, with its *bond* keyword, when its color setting is *type*, to
|
||||
set the color that bonds of each type will be drawn in the image.
|
||||
|
||||
The specified *type* should be an integer from 1 to Nbondtypes = the
|
||||
number of bond types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the *type* argument to specify a range of bond
|
||||
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
|
||||
number of bond types, then an asterisk with no numeric values means
|
||||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
The specified *color* can be a single color which is any of the 140
|
||||
pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option. Or it can be two or more colors separated
|
||||
by a "/" character, e.g. red/green/blue. In the former case, that
|
||||
color is assigned to all the specified bond types. In the latter
|
||||
case, the list of colors are assigned in a round-robin fashion to each
|
||||
of the specified bond types.
|
||||
|
||||
----------
|
||||
|
||||
The *bdiam* keyword can be used with the :doc:`dump image <dump_image>`
|
||||
command, with its *bond* keyword, when its diam setting is *type*, to
|
||||
set the diameter that bonds of each type will be drawn in the image.
|
||||
The specified *type* should be an integer from 1 to Nbondtypes. As
|
||||
with the *bcolor* keyword, a wildcard asterisk can be used as part of
|
||||
the *type* argument to specify a range of bond types. The specified
|
||||
*diam* is the size in whatever distance :doc:`units <units>` you are
|
||||
using, e.g. Angstroms.
|
||||
|
||||
----------
|
||||
|
||||
The *bitrate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the size of the resulting
|
||||
movie file and its quality via setting how many kbits per second are
|
||||
to be used for the movie file. Higher bitrates require less
|
||||
compression and will result in higher quality movies. The quality is
|
||||
also determined by the compression format and encoder. The default
|
||||
setting is 2000 kbit/s, which will result in average quality with
|
||||
older compression formats.
|
||||
|
||||
.. note::
|
||||
|
||||
Not all movie file formats supported by dump movie allow the
|
||||
bitrate to be set. If not, the setting is silently ignored.
|
||||
|
||||
----------
|
||||
|
||||
The *boxcolor* keyword sets the color of the simulation box drawn
|
||||
around the atoms in each image as well as the color of processor
|
||||
sub-domain boundaries. See the "dump image box" command for how to
|
||||
specify that a box be drawn via the *box* keyword, and the sub-domain
|
||||
boundaries via the *subbox* keyword. The color name can be any of the
|
||||
140 pre-defined colors (see below) or a color name defined by the
|
||||
dump_modify color option.
|
||||
|
||||
----------
|
||||
|
||||
The *color* keyword allows definition of a new color name, in addition
|
||||
to the 140-predefined colors (see below), and associates 3
|
||||
red/green/blue RGB values with that color name. The color name can
|
||||
then be used with any other dump_modify keyword that takes a color
|
||||
name as a value. The RGB values should each be floating point values
|
||||
between 0.0 and 1.0 inclusive.
|
||||
|
||||
When a color name is converted to RGB values, the user-defined color
|
||||
names are searched first, then the 140 pre-defined color names. This
|
||||
means you can also use the *color* keyword to overwrite one of the
|
||||
pre-defined color names with new RBG values.
|
||||
|
||||
----------
|
||||
|
||||
The *framerate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the duration of the resulting
|
||||
movie file. Movie files written by the dump *movie* command have a
|
||||
default frame rate of 24 frames per second and the images generated
|
||||
will be converted at that rate. Thus a sequence of 1000 dump images
|
||||
will result in a movie of about 42 seconds. To make a movie run
|
||||
longer you can either generate images more frequently or lower the
|
||||
frame rate. To speed a movie up, you can do the inverse. Using a
|
||||
frame rate higher than 24 is not recommended, as it will result in
|
||||
simply dropping the rendered images. It is more efficient to dump
|
||||
images less frequently.
|
||||
|
||||
----------
|
||||
|
||||
The *header* keyword toggles whether the dump file will include a header.
|
||||
Excluding a header will reduce the size of the dump file for fixes such as
|
||||
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
|
||||
typically written to the header.
|
||||
|
||||
----------
|
||||
|
||||
The COMPRESS package offers both GZ and Zstd compression variants of styles
|
||||
atom, custom, local, cfg, and xyz. When using these styles the compression
|
||||
level can be controlled by the :code:`compression_level` parameter. File names
|
||||
with these styles have to end in either :code:`.gz` or :code:`.zst`.
|
||||
|
||||
GZ supports compression levels from -1 (default), 0 (no compression), and 1 to
|
||||
9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9 as
|
||||
default compression level.
|
||||
GZ supports compression levels from -1 (default), 0 (no compression),
|
||||
and 1 to
|
||||
9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9
|
||||
as default compression level.
|
||||
|
||||
Zstd offers a wider range of compression levels, including negative
|
||||
levels that sacrifice compression for performance. 0 is the
|
||||
default, positive levels are 1 to 22, with 22 being the most expensive
|
||||
levels that sacrifice compression for performance. 0 is the default,
|
||||
positive levels are 1 to 22, with 22 being the most expensive
|
||||
compression. Zstd promises higher compression/decompression speeds for
|
||||
similar compression ratios. For more details see
|
||||
`http://facebook.github.io/zstd/`.
|
||||
|
||||
In addition, Zstd compressed files can have a checksum of the entire
|
||||
contents. The Zstd enabled dump styles enable this feature by default and it
|
||||
can be disabled with the :code:`checksum` parameter.
|
||||
In addition, Zstd compressed files can include a checksum of the
|
||||
entire contents. The Zstd enabled dump styles enable this feature by
|
||||
default and it can be disabled with the :code:`checksum` keyword.
|
||||
|
||||
----------
|
||||
|
||||
@ -1046,100 +745,7 @@ The option defaults are
|
||||
* units = no
|
||||
* unwrap = no
|
||||
|
||||
* acolor = \* red/green/blue/yellow/aqua/cyan
|
||||
* adiam = \* 1.0
|
||||
* amap = min max cf 0.0 2 min blue max red
|
||||
* backcolor = black
|
||||
* bcolor = \* red/green/blue/yellow/aqua/cyan
|
||||
* bdiam = \* 0.5
|
||||
* bitrate = 2000
|
||||
* boxcolor = yellow
|
||||
* color = 140 color names are pre-defined as listed below
|
||||
* framerate = 24
|
||||
|
||||
* compression_level = 9 (gz variants)
|
||||
* compression_level = 0 (zstd variants)
|
||||
* checksum = yes (zstd variants)
|
||||
|
||||
----------
|
||||
|
||||
These are the standard 109 element names that LAMMPS pre-defines for
|
||||
use with the :doc:`dump image <dump_image>` and dump_modify commands.
|
||||
|
||||
* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
|
||||
* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
|
||||
* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
|
||||
* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
|
||||
* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
|
||||
* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
|
||||
* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
|
||||
* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
|
||||
* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
|
||||
* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
|
||||
* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
|
||||
|
||||
----------
|
||||
|
||||
These are the 140 colors that LAMMPS pre-defines for use with the
|
||||
:doc:`dump image <dump_image>` and dump_modify commands. Additional
|
||||
colors can be defined with the dump_modify color command. The 3
|
||||
numbers listed for each name are the RGB (red/green/blue) values.
|
||||
Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
|
||||
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 |
|
||||
+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
|
||||
|
||||
Reference in New Issue
Block a user