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doc/dump_modify.html
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@ -19,7 +19,7 @@
<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
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
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
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
"d" for discrete
"s" for sequential
@ -54,7 +54,7 @@
<I>bdiam</I> args = type diam
type = bond type or range of types (see below)
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
<I>boxcolor</I> arg = color
color = name of color for box lines
@ -109,9 +109,9 @@ parameters are relevant to all dump styles.
<HR>
<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>
keyword, when its color setting is <I>type</I>, to set the color that atoms
of each type will be drawn in the image.
be used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
color setting is <I>type</I>, to set the color that atoms of each type will
be drawn in the image.
</P>
<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
@ -124,23 +124,23 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive).
</P>
<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
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.
case, the list of colors are assigned in a round-robin fashion to each
of the specified atom types.
</P>
<HR>
<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>
keyword, when its diam setting is <I>type</I>, to set the size that atoms
of each type will be drawn in the image. The specified <I>type</I> should
be an integer from 1 to Ntypes. As with the <I>acolor</I> keyword, a
wildcard asterisk can be used as part of the <I>type</I> argument to
specify a range of atomt types. The specified <I>diam</I> is the size in
whatever distance <A HREF = "units.html">units</A> you are using, e.g. Angstroms.
used with the <A HREF = "dump_image.html">dump image</A> command, when its atom
diameter setting is <I>type</I>, to set the size that atoms of each type
will be drawn in the image. The specified <I>type</I> should be an integer
from 1 to Ntypes. As with the <I>acolor</I> keyword, a wildcard asterisk
can be used as part of the <I>type</I> argument to specify a range of atomt
types. The specified <I>diam</I> is the size in whatever distance
<A HREF = "units.html">units</A> the input script is using, e.g. Angstroms.
</P>
<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 =
-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 other options for the mapping mechanism, all of
which are explained on the <A HREF = "dump_modify.html">dump_modify</A> doc page.
procedure.
</P>
<P>There are many possible options for the color map, enabled by the
<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>,
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
<I>hi</I> as <I>max</I> then the range is dynamic, and will the lower and/or
upper bound will be calculated each time an image is drawn.
<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, based
on the set of atoms being visualized.
</P>
<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.
@ -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
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
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.
</P>
<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
<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
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.
@ -224,11 +224,11 @@ to be "purple".
<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>
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
values that overlap. Note that numeric <I>lo</I> and <I>hi</I> 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.
entries can have any <I>lo</I> and <I>hi</I> values and the sub-ranges of
different values can overlap. Note that numeric <I>lo</I> and <I>hi</I> 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.
</P>
<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
@ -284,7 +284,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive).
</P>
<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
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
@ -305,9 +305,9 @@ e.g. Angstroms.
</P>
<HR>
<P>The <I>bgcolor</I> keyword applies only to the dump <I>image</I> style. It sets
the background color of each image. The color name can be any of the
140 pre-defined colors (see below) or a colorname defined by the
<P>The <I>backcolor</I> keyword applies only to the dump <I>image</I> style. It
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.
</P>
<HR>
@ -316,7 +316,22 @@ dump_modify color option.
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
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>
<HR>
@ -511,7 +526,7 @@ box size stored with the snapshot.
<LI>append = no
<LI>bcolor = * red/green/blue/yellow/aqua/cyan
<LI>bdiam = * 0.5
<LI>bgcolor = black
<LI>backcolor = black
<LI>boxcolor = yellow
<LI>color = 140 color names are pre-defined as listed below
<LI>element = "C" for every atom type