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doc/dump_image.html
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@ -13,7 +13,7 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>dump ID group-ID image N file x y z type type keyword value ... <PRE>dump ID group-ID image N file color diameter keyword value ...
</PRE> </PRE>
<UL><LI>ID = user-assigned name for the dump <UL><LI>ID = user-assigned name for the dump
@ -25,18 +25,20 @@
<LI>file = name of file to write image to <LI>file = name of file to write image to
<LI>color = atom attribute that determines color of each atom
<LI>diameter = atom attribute that determines size of each atom
<LI>zero or more keyword/value pairs may be appended <LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I> <LI>keyword = <I>adiam</I> or <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I>
<PRE> <I>atom</I> values = color diam = color and size of atoms <PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
color = <I>none</I> or <I>type</I> or <I>element</I> or atom-attribute <I>atom</I> = yes/no = do or do not draw atoms
diam = number or <I>type</I> or <I>element</I> or atom-attribute <I>bond</I> values = color width = color and width of bonds
number = numeric value for atom diameter (distance units) color = <I>atom</I> or <I>type</I>
<I>bond</I> values = color diam = color and width of bonds width = number or <I>atom</I> or <I>type</I>
color = <I>none</I> or <I>atom</I> or <I>type</I> number = numeric value for bond width (distance units)
diam = number or <I>type</I>
numer = numeric value for bond diameter (distance units)
<I>size</I> values = width height = size of images <I>size</I> values = width height = size of images
width = width of image in # of pixels width = width of image in # of pixels
height = height of image in # of pixels height = height of image in # of pixels
@ -46,7 +48,7 @@
theta or phi can be a variable (see below) theta or phi can be a variable (see below)
<I>center</I> values = flag Cx Cy Cz = center point of image <I>center</I> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below) Cx,Cy,Cz can be variables (see below)
<I>up</I> values = Ux Uy Uz = direction that is "up" in image <I>up</I> values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector Ux,Uy,Uz = components of up vector
@ -66,14 +68,15 @@
diam = diameter of axes lines as fraction of shortest box length diam = diameter of axes lines as fraction of shortest box length
<I>shiny</I> value = factor = shinyness of spheres and cylinders <I>shiny</I> value = factor = shinyness of spheres and cylinders
factor = shinyness of spheres and cylinders from 0.0 to 1.0 factor = shinyness of spheres and cylinders from 0.0 to 1.0
<I>ssao</I> value = yes/no = SSAO depth shading <I>ssao</I> value = yes/no seed = SSAO depth shading
yes/no = turn depth shading on/off yes/no = turn depth shading on/off
seed = random # seed (positive integer)
</PRE> </PRE>
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>dump myDump all image 100 dump.*.jpg <PRE>dump myDump all image 100 dump.*.jpg type type
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
@ -122,21 +125,17 @@ correct ordering.
</P> </P>
<HR> <HR>
<P>The kewords listed above control how the image is rendered. As listed <P>The <I>color</I> and <I>diameter</I> settings determine the color and size of
below, all of the keywords have defaults, most of which you will atoms rendered in the image. They can be any atom attribute defined
likely not need to change. The <A HREF = "dump_modify.html">dump modify</A> also for the <A HREF = "dump.html">dump custom</A> command, including <I>type</I> and
has options specific to the dump image style, particularly for <I>element</I>. This includes per-atom quantities calculated by a
assigning colors to atoms, bonds, and other image features. <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>,
which are prefixed by "c_", "f_", or "v_" respectively. Note that the
<I>diameter</I> setting can be overridden with a numeric value by the
optional <I>adiam</I> keyword, in which case you can specify the <I>diameter</I>
setting with any valid atom attribute.
</P> </P>
<HR> <P>If <I>type</I> is specified for the <I>color</I> setting, then the color of each
<P>The <I>atom</I> keyword determines the color and size of atoms rendered in
the image. If <I>none</I> is specified for the <I>color</I> value (with any
<I>diam</I> value), then no atoms are drawn.
</P>
<P>The <I>color</I> value can be <I>type</I> or <I>element</I> or an atom-attribute.
</P>
<P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
atom is determined by its atom type. By default the mapping of types atom is determined by its atom type. By default the mapping of types
to colors is as follows: to colors is as follows:
</P> </P>
@ -150,25 +149,28 @@ to colors is as follows:
<P>and repeats itself for types > 6. This mapping can be changed by the <P>and repeats itself for types > 6. This mapping can be changed by the
<A HREF = "dump_modify.html">dump_modify acolor</A> command. <A HREF = "dump_modify.html">dump_modify acolor</A> command.
</P> </P>
<P>If <I>element</I> is specified for the <I>color</I> value, then the color of <P>If <I>type</I> is specified for the <I>diameter</I> setting then the diamter of
each atom is determined by which element it is, which in turn is each atom is determined by its atom type. By default all types have
specified by the element-to-type mapping specified by the "dump_modify diameter 1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
element" command. By default every atom type is C (carbon). Every adiam</A> command.
element has a color associated with it, which is the same as the </P>
colors used by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package. <P>If <I>element</I> is specified for the <I>color</I> and/or <I>diameter</I> 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 used by the
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
</P> </P>
<P>An atom-attribute can also be used for the <I>color</I> value. Any <P>If other atom attributes are used for the <I>color</I> or <I>diameter</I>
attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used, settings, they are interpreted in the following way.
e.g. vx, fy, q, spin, etc. This includes per-atom quantities
calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
<A HREF = "variable.html">variable</A>. For example, if "vx" is used as the
per-atom attribute, then the color of the atom will depend on the
x-component of its velocity.
</P> </P>
<P>The association of a per-atom value with a specific color is <P>If "vx", for example, is used as the <I>color</I> setting, then the color
determined by a "color map", which can be specified via the 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
<A HREF = "dump_modify.html">dump_modify</A> command. The basic idea is that the <A HREF = "dump_modify.html">dump_modify</A> command. The basic idea is that the
atom-attribute will be within a range of values, and every value 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 within the range is mapped to a specific color. Depending on how the
@ -176,45 +178,41 @@ 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 that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange". discretely so that the value of -3.2 is "orange".
</P> </P>
<P>The <I>diam</I> value can be a numeric value or <I>type</I> or <I>element</I> or an <P>If "vx", for example, is used as the <I>diameter</I> setting, then the atom
atom-attribute. will be rendered using the x-component of its velocity as the
</P> diameter. If the per-atom value <= 0.0, them the atom will not be
<P>If a numeric value is specified, then all atoms will be drawn with drawn. Note that finite-size spherical particles, as defined by
that diameter, e.g. 1.5, which is in distance units in whatever <A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius or
<A HREF = "units.html">units</A> the input scripts uses, e.g. Angstroms. diameter, which can be used as the <I>diameter</I> setting.
</P>
<P>If <I>type</I> is specified for the diam value then the diamter of each
atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
adiam</A> command.
</P>
<P>If <I>element</I> is specified for the <I>diam</I> value, then the diamater 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 diameter associated with it, which is the same as the
diameters used by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
</P>
<P>An atom-attribute can also be used for the <I>diam</I> value. Any
attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used,
e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
<A HREF = "variable.html">variable</A>. For example, if "vx" is used as the
per-atom attribute, then the diameter of the atom will depend on the
x-component of its velocity, which must be >= 0.0, else the atom will
not be drawn. Note that finite-size spherical particles, as defined
by <A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius,
which can be used as an atom-attribute.
</P> </P>
<HR> <HR>
<P>The <I>bond</I> keyword determines the color and thickness or diameter of <P>The various kewords listed above control how the image is rendered.
bonds rendered in the image. If <I>none</I> is specified for the <I>color</I> As listed below, all of the keywords have defaults, most of which you
value (with any diam value), then no bonds are drawn. will likely not need to change. The <A HREF = "dump_modify.html">dump modify</A>
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
</P> </P>
<P>If <I>atom</I> is specified for the <I>color</I> value, then each bond is drawn <HR>
in 2 halves, with the color of each half being the color of the atom
at that end of the bond. <P>The <I>adiam</I> keyword allows you to override the <I>diameter</I> setting to a
per-atom attribute with a specified numeric value. All atoms will be
drawn with that diameter, e.g. 1.5, which is in whatever distance
<A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
</P>
<P>The <I>atom</I> keyword allow you to turn off the drawing of all atoms,
if the specified value is <I>no</I>.
</P>
<P>By default, no bonds between atoms are drawn in the renedered image.
The <I>bond</I> keyword cause bonds between pairs of atoms (as defined in
the data file read by the <A HREF = "read_data.html">read_data</A> command) to be
drawn with the specified color and width. A bond is only drawn if
both atoms in the bond are part of the group specified with the dump
image command.
</P>
<P>If <I>atom</I> is specified for the bond <I>color</I> value, then each bond is
drawn in 2 halves, with the color of each half being the color of the
atom at that end of the bond.
</P> </P>
<P>If <I>type</I> is specified for the <I>color</I> value, then the color of each <P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
bond is determined by its bond type. By default the mapping of bond bond is determined by its bond type. By default the mapping of bond
@ -230,13 +228,17 @@ types to colors is as follows:
<P>and repeats itself for bond types > 6. This mapping can be changed by <P>and repeats itself for bond types > 6. This mapping can be changed by
the <A HREF = "dump_modify.html">dump_modify bcolor</A> command. the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
</P> </P>
<P>The <I>diam</I> value can be a numeric value or <I>type</I>. <P>The bond <I>width</I> value can be a numeric value or <I>atom</I> or <I>type</I>.
</P> </P>
<P>If a numeric value is specified, then all bond will be drawn with that <P>If a numeric value is specified, then all bonds will be drawn as
diameter, e.g. 1.0, which is in distance units in whatever cylinders with that diameter, e.g. 1.0, which is in whatever distance
<A HREF = "units.html">units</A> the input script uses, e.g. Angstroms. <A HREF = "units.html">units</A> the input script defines, e.g. Angstroms.
</P> </P>
<P>If <I>type</I> is specified for the <I>diam</I> value then the color of each <P>If <I>atom</I> is specified for the <I>width</I> value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.
</P>
<P>If <I>type</I> is specified for the <I>width</I> value then the diameter of each
bond is determined by its bond type. By default all types have bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify diameter 0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
bdiam</A> command. bdiam</A> command.
@ -340,9 +342,10 @@ a rough non-shiny surface.
</P> </P>
<P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion <P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If <I>yes</I> is set, then atoms further (SSAO) model for depth shading. If <I>yes</I> is set, then atoms further
away from the viewer are darkened, which is perceived as depth. The away from the viewer are darkened via a randomized process, which is
calculation of this effect can increase the cost of computing the perceived as depth. The calculation of this effect can increase the
image by roughly 2x. If <I>no</I> is set, no depth shading is performed. cost of computing the image by roughly 2x. If <I>no</I> is set, no depth
shading is performed.
</P> </P>
<HR> <HR>

173
doc/dump_image.txt
View File

@ -10,23 +10,23 @@ dump image command :h3
[Syntax:] [Syntax:]
dump ID group-ID image N file x y z type type keyword value ... :pre dump ID group-ID image N file color diameter keyword value ... :pre
ID = user-assigned name for the dump :ulb,l ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l group-ID = ID of the group of atoms to be imaged :l
image = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l image = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l N = dump every this many timesteps :l
file = name of file to write image to :l file = name of file to write image to :l
color = atom attribute that determines color of each atom :l
diameter = atom attribute that determines size of each atom :l
zero or more keyword/value pairs may be appended :l zero or more keyword/value pairs may be appended :l
keyword = {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
{atom} values = color diam = color and size of atoms {adiam} value = number = numeric value for atom diameter (distance units)
color = {none} or {type} or {element} or atom-attribute {atom} = yes/no = do or do not draw atoms
diam = number or {type} or {element} or atom-attribute {bond} values = color width = color and width of bonds
number = numeric value for atom diameter (distance units) color = {atom} or {type}
{bond} values = color diam = color and width of bonds width = number or {atom} or {type}
color = {none} or {atom} or {type} number = numeric value for bond width (distance units)
diam = number or {type}
numer = numeric value for bond diameter (distance units)
{size} values = width height = size of images {size} values = width height = size of images
width = width of image in # of pixels width = width of image in # of pixels
height = height of image in # of pixels height = height of image in # of pixels
@ -36,7 +36,7 @@ keyword = {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or
theta or phi can be a variable (see below) theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image {center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below) Cx,Cy,Cz can be variables (see below)
{up} values = Ux Uy Uz = direction that is "up" in image {up} values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector Ux,Uy,Uz = components of up vector
@ -56,13 +56,14 @@ keyword = {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or
diam = diameter of axes lines as fraction of shortest box length diam = diameter of axes lines as fraction of shortest box length
{shiny} value = factor = shinyness of spheres and cylinders {shiny} value = factor = shinyness of spheres and cylinders
factor = shinyness of spheres and cylinders from 0.0 to 1.0 factor = shinyness of spheres and cylinders from 0.0 to 1.0
{ssao} value = yes/no = SSAO depth shading {ssao} value = yes/no seed = SSAO depth shading
yes/no = turn depth shading on/off :pre yes/no = turn depth shading on/off
seed = random # seed (positive integer) :pre
:ule :ule
[Examples:] [Examples:]
dump myDump all image 100 dump.*.jpg :pre dump myDump all image 100 dump.*.jpg type type :pre
[Description:] [Description:]
@ -111,21 +112,17 @@ correct ordering.
:line :line
The kewords listed above control how the image is rendered. As listed The {color} and {diameter} settings determine the color and size of
below, all of the keywords have defaults, most of which you will atoms rendered in the image. They can be any atom attribute defined
likely not need to change. The "dump modify"_dump_modify.html also for the "dump custom"_dump.html command, including {type} and
has options specific to the dump image style, particularly for {element}. This includes per-atom quantities calculated by a
assigning colors to atoms, bonds, and other image features. "compute"_compute.html, "fix"_fix.html, or "variable"_variable.html,
which are prefixed by "c_", "f_", or "v_" respectively. Note that the
{diameter} setting can be overridden with a numeric value by the
optional {adiam} keyword, in which case you can specify the {diameter}
setting with any valid atom attribute.
:line If {type} is specified for the {color} setting, then the color of each
The {atom} keyword determines the color and size of atoms rendered in
the image. If {none} is specified for the {color} value (with any
{diam} value), then no atoms are drawn.
The {color} value can be {type} or {element} or an atom-attribute.
If {type} is specified for the {color} value, then the color of each
atom is determined by its atom type. By default the mapping of types atom is determined by its atom type. By default the mapping of types
to colors is as follows: to colors is as follows:
@ -139,25 +136,28 @@ type 6 = cyan :ul
and repeats itself for types > 6. This mapping can be changed by the and repeats itself for types > 6. This mapping can be changed by the
"dump_modify acolor"_dump_modify.html command. "dump_modify acolor"_dump_modify.html command.
If {element} is specified for the {color} value, then the color of If {type} is specified for the {diameter} setting then the diamter of
each atom is determined by which element it is, which in turn is each atom is determined by its atom type. By default all types have
specified by the element-to-type mapping specified by the "dump_modify diameter 1.0. This mapping can be changed by the "dump_modify
element" command. By default every atom type is C (carbon). Every adiam"_dump_modify.html command.
element has a color associated with it, which is the same as the
colors used by the "AtomEye"_atomeye visualization package. 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 used by the
"AtomEye"_atomeye visualization package.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
An atom-attribute can also be used for the {color} value. Any If other atom attributes are used for the {color} or {diameter}
attribute listed on the "dump custom"_dump.html doc page can be used, settings, they are interpreted in the following way.
e.g. vx, fy, q, spin, etc. This includes per-atom quantities
calculated by a "compute"_compute.html, "fix"_fix.html, or
"variable"_variable.html. For example, if "vx" is used as the
per-atom attribute, 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 If "vx", for example, is used as the {color} setting, then the color
determined by a "color map", which can be specified via the 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"_dump_modify.html command. The basic idea is that the "dump_modify"_dump_modify.html command. The basic idea is that the
atom-attribute will be within a range of values, and every value 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 within the range is mapped to a specific color. Depending on how the
@ -165,45 +165,41 @@ 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 that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange". discretely so that the value of -3.2 is "orange".
The {diam} value can be a numeric value or {type} or {element} or an If "vx", for example, is used as the {diameter} setting, then the atom
atom-attribute. 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
If a numeric value is specified, then all atoms will be drawn with drawn. Note that finite-size spherical particles, as defined by
that diameter, e.g. 1.5, which is in distance units in whatever "atom_style sphere"_atom_style.html define a per-particle radius or
"units"_units.html the input scripts uses, e.g. Angstroms. diameter, which can be used as the {diameter} setting.
If {type} is specified for the diam value then the diamter 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"_dump_modify.html command.
If {element} is specified for the {diam} value, then the diamater 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 diameter associated with it, which is the same as the
diameters used by the "AtomEye"_atomeye visualization package.
An atom-attribute can also be used for the {diam} value. Any
attribute listed on the "dump custom"_dump.html doc page can be used,
e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
calculated by a "compute"_compute.html, "fix"_fix.html, or
"variable"_variable.html. For example, if "vx" is used as the
per-atom attribute, then the diameter of the atom will depend on the
x-component of its velocity, which must be >= 0.0, else the atom will
not be drawn. Note that finite-size spherical particles, as defined
by "atom_style sphere"_atom_style.html define a per-particle radius,
which can be used as an atom-attribute.
:line :line
The {bond} keyword determines the color and thickness or diameter of The various kewords listed above control how the image is rendered.
bonds rendered in the image. If {none} is specified for the {color} As listed below, all of the keywords have defaults, most of which you
value (with any diam value), then no bonds are drawn. will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
If {atom} is specified for the {color} value, then each bond is drawn :line
in 2 halves, with the color of each half being the color of the atom
at that end of the bond. The {adiam} keyword allows you to override the {diameter} setting to a
per-atom attribute with a specified numeric value. All atoms will be
drawn with that diameter, e.g. 1.5, which is in whatever distance
"units"_units.html the input script defines, e.g. Angstroms.
The {atom} keyword allow you to turn off the drawing of all atoms,
if the specified value is {no}.
By default, no bonds between atoms are drawn in the renedered image.
The {bond} keyword cause bonds between pairs of atoms (as defined in
the data file read by the "read_data"_read_data.html command) to be
drawn with the specified color and width. A bond is only drawn if
both atoms in the bond are part of the group specified with the dump
image command.
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 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 bond is determined by its bond type. By default the mapping of bond
@ -219,13 +215,17 @@ type 6 = cyan :ul
and repeats itself for bond types > 6. This mapping can be changed by and repeats itself for bond types > 6. This mapping can be changed by
the "dump_modify bcolor"_dump_modify.html command. the "dump_modify bcolor"_dump_modify.html command.
The {diam} value can be a numeric value or {type}. The bond {width} value can be a numeric value or {atom} or {type}.
If a numeric value is specified, then all bond will be drawn with that If a numeric value is specified, then all bonds will be drawn as
diameter, e.g. 1.0, which is in distance units in whatever cylinders with that diameter, e.g. 1.0, which is in whatever distance
"units"_units.html the input script uses, e.g. Angstroms. "units"_units.html the input script defines, e.g. Angstroms.
If {type} is specified for the {diam} value then the color of each 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 bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the "dump_modify diameter 0.5. This mapping can be changed by the "dump_modify
bdiam"_dump_modify.html command. bdiam"_dump_modify.html command.
@ -329,9 +329,10 @@ a rough non-shiny surface.
The {ssao} keyword turns on/off a screen space ambient occlusion The {ssao} keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If {yes} is set, then atoms further (SSAO) model for depth shading. If {yes} is set, then atoms further
away from the viewer are darkened, which is perceived as depth. The away from the viewer are darkened via a randomized process, which is
calculation of this effect can increase the cost of computing the perceived as depth. The calculation of this effect can increase the
image by roughly 2x. If {no} is set, no depth shading is performed. cost of computing the image by roughly 2x. If {no} is set, no depth
shading is performed.
:line :line

81
doc/dump_modify.html
View File

@ -19,7 +19,7 @@
<LI>one or more keyword/value pairs may be appended <LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>acolor</I> or <I>adiam</I> or <I>amap</I> or <I>append</I> or <I>bcolor</I> or <I>bdiam</I> or <I>bgcolor</I> or <I>boxcolor</I> or <I>color</I> or <I>every</I> or <I>flush</I> or <I>format</I> or <I>image</I> or <I>label</I> or <I>precision</I> or <I>region</I> or <I>scale</I> or <I>sort</I> or <I>thresh</I> or <I>unwrap</I> <LI>keyword = <I>acolor</I> or <I>adiam</I> or <I>amap</I> or <I>append</I> or <I>bcolor</I> or <I>bdiam</I> or <I>backcolor</I> or <I>boxcolor</I> or <I>color</I> or <I>every</I> or <I>flush</I> or <I>format</I> or <I>image</I> or <I>label</I> or <I>precision</I> or <I>region</I> or <I>scale</I> or <I>sort</I> or <I>thresh</I> or <I>unwrap</I>
<PRE> <I>acolor</I> args = type color <PRE> <I>acolor</I> args = type color
type = atom type or range of types (see below) type = atom type or range of types (see below)
@ -30,7 +30,7 @@
<I>amap</I> args = lo hi style N delta entry1 entry2 ... entryN <I>amap</I> args = lo hi style N delta entry1 entry2 ... entryN
lo = number or <I>min</I> = lower bound of range of color map lo = number or <I>min</I> = lower bound of range of color map
hi = number or <I>max</I> = upper bound of range of color map hi = number or <I>max</I> = upper bound of range of color map
style = 2 letters = "b" or "c" or "s" plus "a" or "f" style = 2 letters = "c" or "d" or "s" plus "a" or "f"
"c" for continuous "c" for continuous
"d" for discrete "d" for discrete
"s" for sequential "s" for sequential
@ -54,7 +54,7 @@
<I>bdiam</I> args = type diam <I>bdiam</I> args = type diam
type = bond type or range of types (see below) type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units) diam = diameter of bonds of that type (distance units)
<I>bgcolor</I> arg = color <I>backcolor</I> arg = color
color = name of color for background color = name of color for background
<I>boxcolor</I> arg = color <I>boxcolor</I> arg = color
color = name of color for box lines color = name of color for box lines
@ -109,9 +109,9 @@ parameters are relevant to all dump styles.
<HR> <HR>
<P>The <I>acolor</I> keyword applies only to the dump <I>image</I> style. It can <P>The <I>acolor</I> keyword applies only to the dump <I>image</I> style. It can
be used with the <A HREF = "dump_image.html">dump image</A> command, with its <I>atom</I> be used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
keyword, when its color setting is <I>type</I>, to set the color that atoms color setting is <I>type</I>, to set the color that atoms of each type will
of each type will be drawn in the image. be drawn in the image.
</P> </P>
<P>The specified <I>type</I> should be an integer from 1 to Ntypes = the <P>The specified <I>type</I> should be an integer from 1 to Ntypes = the
number of atom types. A wildcard asterisk can be used in place of or number of atom types. A wildcard asterisk can be used in place of or
@ -124,23 +124,23 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). (inclusive).
</P> </P>
<P>The specified <I>color</I> can be a single color which is any of the 140 <P>The specified <I>color</I> can be a single color which is any of the 140
pre-defined colors (see below) or a colorname defined by the 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 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 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 color is assigned to all the specified atom types. In the latter
case, the list of colors are assigned in a round-robin fashion case, the list of colors are assigned in a round-robin fashion to each
to each of the specified atom types. of the specified atom types.
</P> </P>
<HR> <HR>
<P>The <I>adiam</I> keyword applies only to the dump <I>image</I> style. It can be <P>The <I>adiam</I> keyword applies only to the dump <I>image</I> style. It can be
used with the <A HREF = "dump_image.html">dump image</A> command, with its <I>atom</I> used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
keyword, when its diam setting is <I>type</I>, to set the size that atoms diameter setting is <I>type</I>, to set the size that atoms of each type
of each type will be drawn in the image. The specified <I>type</I> should will be drawn in the image. The specified <I>type</I> should be an integer
be an integer from 1 to Ntypes. As with the <I>acolor</I> keyword, a from 1 to Ntypes. As with the <I>acolor</I> keyword, a wildcard asterisk
wildcard asterisk can be used as part of the <I>type</I> argument to can be used as part of the <I>type</I> argument to specify a range of atomt
specify a range of atomt types. The specified <I>diam</I> is the size in types. The specified <I>diam</I> is the size in whatever distance
whatever distance <A HREF = "units.html">units</A> you are using, e.g. Angstroms. <A HREF = "units.html">units</A> the input script is using, e.g. Angstroms.
</P> </P>
<HR> <HR>
@ -157,8 +157,7 @@ within a range of values, and that range is associated with a a series
of colors (e.g. red, blue, green). An atom's specific value (vx = 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 -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 red and blue), and a specific color is determined via an interpolation
procedure. There are other options for the mapping mechanism, all of procedure.
which are explained on the <A HREF = "dump_modify.html">dump_modify</A> doc page.
</P> </P>
<P>There are many possible options for the color map, enabled by the <P>There are many possible options for the color map, enabled by the
<I>amap</I> keyword. Here are the details. <I>amap</I> keyword. Here are the details.
@ -167,8 +166,9 @@ which are explained on the <A HREF = "dump_modify.html">dump_modify</A> doc page
the atom attribute. If numeric values are used for <I>lo</I> and/or <I>hi</I>, the atom attribute. If numeric values are used for <I>lo</I> and/or <I>hi</I>,
then values that are lower/higher than that value are set to the then values that are lower/higher than that value are set to the
value. I.e. the range is static. If <I>lo</I> is specified as <I>min</I> or value. I.e. the range is static. If <I>lo</I> is specified as <I>min</I> or
<I>hi</I> as <I>max</I> then the range is dynamic, and will the lower and/or <I>hi</I> as <I>max</I> then the range is dynamic, and the lower and/or
upper bound will be calculated each time an image is drawn. upper bound will be calculated each time an image is drawn, based
on the set of atoms being visualized.
</P> </P>
<P>The <I>style</I> setting is two letters, such as "ca". The first letter is <P>The <I>style</I> setting is two letters, such as "ca". The first letter is
either "c" for continuous, "d" for discrete, or "s" for sequential. either "c" for continuous, "d" for discrete, or "s" for sequential.
@ -200,13 +200,13 @@ from -9.0 <= color2 < -8.0, etc.
<P>The <I>N</I> setting is how many entries follow. The format of the entries <P>The <I>N</I> setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or depends on whether the color map style is continuous, discrete or
sequential. In all cases the <I>color</I> setting can be any of the 140 sequential. In all cases the <I>color</I> setting can be any of the 140
pre-defined colors (see below) or a colorname defined by the pre-defined colors (see below) or a color name defined by the
dump_modify color option. dump_modify color option.
</P> </P>
<P>For continuous color maps, each entry has a <I>value</I> and a <I>color</I>. <P>For continuous color maps, each entry has a <I>value</I> and a <I>color</I>.
The <I>value</I> is either a number within the range of values or <I>min</I> or The <I>value</I> is either a number within the range of values or <I>min</I> or
<I>max</I>. The <I>value</I> of the first entry must be <I>min</I> and the <I>value</I> <I>max</I>. The <I>value</I> of the first entry must be <I>min</I> and the <I>value</I>
of hte last entry must be <I>max</I>. Any entries in between must have of the last entry must be <I>max</I>. Any entries in between must have
increasing values. Note that numeric values can be specified either increasing values. Note that numeric values can be specified either
as absolute numbers or as fractions (0.0 to 1.0) of the range, 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. depending on the "a" or "f" in the style setting for the color map.
@ -224,11 +224,11 @@ to be "purple".
<I>color</I>. The <I>lo</I> and <I>hi</I> settings are either numbers within the <I>color</I>. The <I>lo</I> and <I>hi</I> settings are either numbers within the
range of values or <I>lo</I> can be <I>min</I> or <I>hi</I> can be <I>max</I>. The <I>lo</I> range of values or <I>lo</I> can be <I>min</I> or <I>hi</I> can be <I>max</I>. The <I>lo</I>
and <I>hi</I> settings of the last entry must be <I>min</I> and <I>max</I>. Other and <I>hi</I> settings of the last entry must be <I>min</I> and <I>max</I>. Other
entries can have any <I>lo</I> and <I>hi</I> values, including sub-ranges of entries can have any <I>lo</I> and <I>hi</I> values and the sub-ranges of
values that overlap. Note that numeric <I>lo</I> and <I>hi</I> values can be different values can overlap. Note that numeric <I>lo</I> and <I>hi</I> values
specified either as absolute numbers or as fractions (0.0 to 1.0) of can be specified either as absolute numbers or as fractions (0.0 to
the range, depending on the "a" or "f" in the style setting for the 1.0) of the range, depending on the "a" or "f" in the style setting
color map. for the color map.
</P> </P>
<P>Here is how the entries are used to determine the color of an <P>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 individual atom, given the value X of its atom attribute. The entries
@ -284,7 +284,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). (inclusive).
</P> </P>
<P>The specified <I>color</I> can be a single color which is any of the 140 <P>The specified <I>color</I> can be a single color which is any of the 140
pre-defined colors (see below) or a colorname defined by the 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 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 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 color is assigned to all the specified bond types. In the latter
@ -305,9 +305,9 @@ e.g. Angstroms.
</P> </P>
<HR> <HR>
<P>The <I>bgcolor</I> keyword applies only to the dump <I>image</I> style. It sets <P>The <I>backcolor</I> keyword applies only to the dump <I>image</I> style. It
the background color of each image. The color name can be any of the sets the background color of the images. The color name can be any of
140 pre-defined colors (see below) or a colorname defined by the the 140 pre-defined colors (see below) or a color name defined by the
dump_modify color option. dump_modify color option.
</P> </P>
<HR> <HR>
@ -316,7 +316,22 @@ dump_modify color option.
sets the color of the simulation box drawn around the atoms in each sets the color of the simulation box drawn around the atoms in each
image. See the "dump image box" command for how to specify that a box image. See the "dump image box" command for how to specify that a box
be drawn. The color name can be any of the 140 pre-defined colors be drawn. The color name can be any of the 140 pre-defined colors
(see below) or a colorname defined by the dump_modify color option. (see below) or a color name defined by the dump_modify color option.
</P>
<HR>
<P>The <I>color</I> keyword applies only to the dump <I>image</I> style. It 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.
</P>
<P>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 <I>color</I> keyword to overwrite one of the
pre-defined color names with new RBG values.
</P> </P>
<HR> <HR>
@ -511,7 +526,7 @@ box size stored with the snapshot.
<LI>append = no <LI>append = no
<LI>bcolor = * red/green/blue/yellow/aqua/cyan <LI>bcolor = * red/green/blue/yellow/aqua/cyan
<LI>bdiam = * 0.5 <LI>bdiam = * 0.5
<LI>bgcolor = black <LI>backcolor = black
<LI>boxcolor = yellow <LI>boxcolor = yellow
<LI>color = 140 color names are pre-defined as listed below <LI>color = 140 color names are pre-defined as listed below
<LI>element = "C" for every atom type <LI>element = "C" for every atom type

81
doc/dump_modify.txt
View File

@ -14,7 +14,7 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l one or more keyword/value pairs may be appended :l
keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {bgcolor} or {boxcolor} or {color} or {every} or {flush} or {format} or {image} or {label} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {backcolor} or {boxcolor} or {color} or {every} or {flush} or {format} or {image} or {label} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{acolor} args = type color {acolor} args = type color
type = atom type or range of types (see below) type = atom type or range of types (see below)
color = name of color or color1/color2/... color = name of color or color1/color2/...
@ -24,7 +24,7 @@ keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {b
{amap} args = lo hi style N delta entry1 entry2 ... entryN {amap} args = lo hi style N delta entry1 entry2 ... entryN
lo = number or {min} = lower bound of range of color map lo = number or {min} = lower bound of range of color map
hi = number or {max} = upper bound of range of color map hi = number or {max} = upper bound of range of color map
style = 2 letters = "b" or "c" or "s" plus "a" or "f" style = 2 letters = "c" or "d" or "s" plus "a" or "f"
"c" for continuous "c" for continuous
"d" for discrete "d" for discrete
"s" for sequential "s" for sequential
@ -48,7 +48,7 @@ keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {b
{bdiam} args = type diam {bdiam} args = type diam
type = bond type or range of types (see below) type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units) diam = diameter of bonds of that type (distance units)
{bgcolor} arg = color {backcolor} arg = color
color = name of color for background color = name of color for background
{boxcolor} arg = color {boxcolor} arg = color
color = name of color for box lines color = name of color for box lines
@ -102,9 +102,9 @@ parameters are relevant to all dump styles.
:line :line
The {acolor} keyword applies only to the dump {image} style. It can The {acolor} keyword applies only to the dump {image} style. It can
be used with the "dump image"_dump_image.html command, with its {atom} be used with the "dump image"_dump_image.html command, when its atom
keyword, when its color setting is {type}, to set the color that atoms color setting is {type}, to set the color that atoms of each type will
of each type will be drawn in the image. be drawn in the image.
The specified {type} should be an integer from 1 to Ntypes = the 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 number of atom types. A wildcard asterisk can be used in place of or
@ -117,23 +117,23 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). (inclusive).
The specified {color} can be a single color which is any of the 140 The specified {color} can be a single color which is any of the 140
pre-defined colors (see below) or a colorname defined by the 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 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 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 color is assigned to all the specified atom types. In the latter
case, the list of colors are assigned in a round-robin fashion case, the list of colors are assigned in a round-robin fashion to each
to each of the specified atom types. of the specified atom types.
:line :line
The {adiam} keyword applies only to the dump {image} style. It can be The {adiam} keyword applies only to the dump {image} style. It can be
used with the "dump image"_dump_image.html command, with its {atom} used with the "dump image"_dump_image.html command, when its atom
keyword, when its diam setting is {type}, to set the size that atoms diameter setting is {type}, to set the size that atoms of each type
of each type will be drawn in the image. The specified {type} should will be drawn in the image. The specified {type} should be an integer
be an integer from 1 to Ntypes. As with the {acolor} keyword, a from 1 to Ntypes. As with the {acolor} keyword, a wildcard asterisk
wildcard asterisk can be used as part of the {type} argument to can be used as part of the {type} argument to specify a range of atomt
specify a range of atomt types. The specified {diam} is the size in types. The specified {diam} is the size in whatever distance
whatever distance "units"_units.html you are using, e.g. Angstroms. "units"_units.html the input script is using, e.g. Angstroms.
:line :line
@ -150,8 +150,7 @@ within a range of values, and that range is associated with a a series
of colors (e.g. red, blue, green). An atom's specific value (vx = 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 -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 red and blue), and a specific color is determined via an interpolation
procedure. There are other options for the mapping mechanism, all of procedure.
which are explained on the "dump_modify"_dump_modify.html doc page.
There are many possible options for the color map, enabled by the There are many possible options for the color map, enabled by the
{amap} keyword. Here are the details. {amap} keyword. Here are the details.
@ -160,8 +159,9 @@ 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}, 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 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 value. I.e. the range is static. If {lo} is specified as {min} or
{hi} as {max} then the range is dynamic, and will the lower and/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. 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 The {style} setting is two letters, such as "ca". The first letter is
either "c" for continuous, "d" for discrete, or "s" for sequential. either "c" for continuous, "d" for discrete, or "s" for sequential.
@ -193,13 +193,13 @@ from -9.0 <= color2 < -8.0, etc.
The {N} setting is how many entries follow. The format of the entries The {N} setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or depends on whether the color map style is continuous, discrete or
sequential. In all cases the {color} setting can be any of the 140 sequential. In all cases the {color} setting can be any of the 140
pre-defined colors (see below) or a colorname defined by the pre-defined colors (see below) or a color name defined by the
dump_modify color option. dump_modify color option.
For continuous color maps, each entry has a {value} and a {color}. 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 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} {max}. The {value} of the first entry must be {min} and the {value}
of hte last entry must be {max}. Any entries in between must have of the last entry must be {max}. Any entries in between must have
increasing values. Note that numeric values can be specified either increasing values. Note that numeric values can be specified either
as absolute numbers or as fractions (0.0 to 1.0) of the range, 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. depending on the "a" or "f" in the style setting for the color map.
@ -217,11 +217,11 @@ 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 {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} 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 and {hi} settings of the last entry must be {min} and {max}. Other
entries can have any {lo} and {hi} values, including sub-ranges of entries can have any {lo} and {hi} values and the sub-ranges of
values that overlap. Note that numeric {lo} and {hi} values can be different values can overlap. Note that numeric {lo} and {hi} values
specified either as absolute numbers or as fractions (0.0 to 1.0) of can be specified either as absolute numbers or as fractions (0.0 to
the range, depending on the "a" or "f" in the style setting for the 1.0) of the range, depending on the "a" or "f" in the style setting
color map. for the color map.
Here is how the entries are used to determine the color of an 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 individual atom, given the value X of its atom attribute. The entries
@ -277,7 +277,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). (inclusive).
The specified {color} can be a single color which is any of the 140 The specified {color} can be a single color which is any of the 140
pre-defined colors (see below) or a colorname defined by the 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 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 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 color is assigned to all the specified bond types. In the latter
@ -298,9 +298,9 @@ e.g. Angstroms.
:line :line
The {bgcolor} keyword applies only to the dump {image} style. It sets The {backcolor} keyword applies only to the dump {image} style. It
the background color of each image. The color name can be any of the sets the background color of the images. The color name can be any of
140 pre-defined colors (see below) or a colorname defined by the the 140 pre-defined colors (see below) or a color name defined by the
dump_modify color option. dump_modify color option.
:line :line
@ -309,7 +309,22 @@ The {boxcolor} keyword applies only to the dump {image} style. It
sets the color of the simulation box drawn around the atoms in each sets the color of the simulation box drawn around the atoms in each
image. See the "dump image box" command for how to specify that a box image. See the "dump image box" command for how to specify that a box
be drawn. The color name can be any of the 140 pre-defined colors be drawn. The color name can be any of the 140 pre-defined colors
(see below) or a colorname defined by the dump_modify color option. (see below) or a color name defined by the dump_modify color option.
:line
The {color} keyword applies only to the dump {image} style. It 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.
:line :line
@ -504,7 +519,7 @@ amap = min max cf 2 0.0 blue 1.0 red
append = no append = no
bcolor = * red/green/blue/yellow/aqua/cyan bcolor = * red/green/blue/yellow/aqua/cyan
bdiam = * 0.5 bdiam = * 0.5
bgcolor = black backcolor = black
boxcolor = yellow boxcolor = yellow
color = 140 color names are pre-defined as listed below color = 140 color names are pre-defined as listed below
element = "C" for every atom type element = "C" for every atom type

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@ -83,8 +83,8 @@ when they are output in <A HREF = "dump.html">dump</A> files. It can be useful
debugging purposes; i.e. positioning an atom at a precise location to debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy. compute subsequent forces or energy.
</P> </P>
<P>The style <I>atom</I> selects one or more atoms in a range of atom IDs. <P>The style <I>atom</I> selects all the atoms in a range of atom IDs. The
The style <I>type</I> selects all the atoms in a range of types. The style style <I>type</I> selects all the atoms in a range of types. The style
<I>mol</I> selects all the atoms in a range of molecule IDs. <I>mol</I> selects all the atoms in a range of molecule IDs.
</P> </P>
<P>In each of the range cases, a single value can be specified, or a <P>In each of the range cases, a single value can be specified, or a

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@ -78,8 +78,8 @@ when they are output in "dump"_dump.html files. It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy. compute subsequent forces or energy.
The style {atom} selects one or more atoms in a range of atom IDs. The style {atom} selects all the atoms in a range of atom IDs. The
The style {type} selects all the atoms in a range of types. The style style {type} selects all the atoms in a range of types. The style
{mol} selects all the atoms in a range of molecule IDs. {mol} selects all the atoms in a range of molecule IDs.
In each of the range cases, a single value can be specified, or a In each of the range cases, a single value can be specified, or a