Syntax:
-dump ID group-ID image N file x y z type type keyword value ... +dump ID group-ID image N file color diameter keyword value ...
atom values = color diam = color and size of atoms
- color = none or type or element or atom-attribute
- diam = number or type or element or atom-attribute
- number = numeric value for atom diameter (distance units)
- bond values = color diam = color and width of bonds
- color = none or atom or type
- diam = number or type
- numer = numeric value for bond diameter (distance units)
+ adiam value = number = numeric value for atom diameter (distance units)
+ atom = yes/no = do or do not draw atoms
+ bond values = color width = color and width of bonds
+ color = atom or type
+ width = number or atom or type
+ number = numeric value for bond width (distance units)
size values = width height = size of images
width = width 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)
center values = flag Cx Cy Cz = center point of image
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)
up values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
@@ -66,14 +68,15 @@
diam = diameter of axes lines as fraction of shortest box length
shiny value = factor = shinyness of spheres and cylinders
factor = shinyness of spheres and cylinders from 0.0 to 1.0
- ssao value = yes/no = SSAO depth shading
- yes/no = turn depth shading on/off
+ ssao value = yes/no seed = SSAO depth shading
+ yes/no = turn depth shading on/off
+ seed = random # seed (positive integer)
Examples:
-dump myDump all image 100 dump.*.jpg +dump myDump all image 100 dump.*.jpg type typeDescription:
@@ -122,21 +125,17 @@ correct ordering.
-The kewords listed above control how the image is rendered. As listed -below, all of the keywords have defaults, most of which you will -likely not need to change. The dump modify also -has options specific to the dump image style, particularly for -assigning colors to atoms, bonds, and other image features. +
The color and diameter settings determine the color and size of +atoms rendered in the image. They can be any atom attribute defined +for the dump custom command, including type and +element. This includes per-atom quantities calculated by a +compute, fix, or variable, +which are prefixed by "c_", "f_", or "v_" respectively. Note that the +diameter setting can be overridden with a numeric value by the +optional adiam keyword, in which case you can specify the diameter +setting with any valid atom attribute.
-
- -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 +
If type is specified for the color setting, then the color of each atom is determined by its atom type. By default the mapping of types to colors is as follows:
@@ -150,25 +149,28 @@ to colors is as follows:and repeats itself for types > 6. This mapping can be changed by the dump_modify acolor command.
-If element is specified for the color value, then the color 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 associated with it, which is the same as the -colors used by the AtomEye visualization package. +
If type is specified for the diameter setting 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 command. +
+If element is specified for the color and/or diameter setting, +then the color and/or diameter of each atom is determined by which +element it is, which in turn is specified by the element-to-type +mapping specified by the "dump_modify element" command. By default +every atom type is C (carbon). Every element has a color and diameter +associated with it, which is the same as the colors used by the +AtomEye visualization package.
-An atom-attribute can also be used for the color value. Any -attribute listed on the dump custom doc page can be used, -e.g. vx, fy, q, spin, etc. This includes per-atom quantities -calculated by a compute, fix, or -variable. 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. +
If other atom attributes are used for the color or diameter +settings, they are interpreted in the following way.
-The association of a per-atom value with a specific color is -determined by a "color map", which can be specified via the +
If "vx", for example, is used as the color setting, then the color +of the atom will depend on the x-component of its velocity. The +association of a per-atom value with a specific color is determined by +a "color map", which can be specified via the dump_modify command. The basic idea is that the atom-attribute will be within a range of values, and every value within the range is mapped to a specific color. Depending on how the @@ -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 discretely so that the value of -3.2 is "orange".
-The diam value can be a numeric value or type or element or an -atom-attribute. -
-If a numeric value is specified, then all atoms will be drawn with -that diameter, e.g. 1.5, which is in distance units in whatever -units the input scripts uses, e.g. Angstroms. -
-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 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 visualization package. -
-An atom-attribute can also be used for the diam value. Any -attribute listed on the dump custom doc page can be used, -e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities -calculated by a compute, fix, or -variable. 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 define a per-particle radius, -which can be used as an atom-attribute. +
If "vx", for example, is used as the diameter setting, then the atom +will be rendered using the x-component of its velocity as the +diameter. If the per-atom value <= 0.0, them the atom will not be +drawn. Note that finite-size spherical particles, as defined by +atom_style sphere define a per-particle radius or +diameter, which can be used as the diameter setting.
-The bond keyword determines the color and thickness or diameter of -bonds rendered in the image. If none is specified for the color -value (with any diam value), then no bonds are drawn. +
The various kewords listed above control how the image is rendered. +As listed below, all of the keywords have defaults, most of which you +will likely not need to change. The dump modify +also has options specific to the dump image style, particularly for +assigning colors to atoms, bonds, and other image features.
-If atom is specified for the 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. +
+ +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 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 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 bond is determined by its bond type. By default the mapping of bond @@ -230,13 +228,17 @@ types to colors is as follows:
and repeats itself for bond types > 6. This mapping can be changed by the dump_modify bcolor 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 -diameter, e.g. 1.0, which is in distance units in whatever -units the input script uses, e.g. Angstroms. +
If a numeric value is specified, then all bonds will be drawn as +cylinders with that diameter, e.g. 1.0, which is in whatever distance +units the input script defines, e.g. Angstroms.
-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 diameter 0.5. This mapping can be changed by the dump_modify bdiam command. @@ -340,9 +342,10 @@ a rough non-shiny surface.
The ssao keyword turns on/off a screen space ambient occlusion (SSAO) model for depth shading. If yes is set, then atoms further -away from the viewer are darkened, which is perceived as depth. The -calculation of this effect can increase the cost of computing the -image by roughly 2x. If no is set, no depth shading is performed. +away from the viewer are darkened via a randomized process, which is +perceived as depth. The calculation of this effect can increase the +cost of computing the image by roughly 2x. If no is set, no depth +shading is performed.
diff --git a/doc/dump_image.txt b/doc/dump_image.txt index 5e9521760a..92ed938ad6 100644 --- a/doc/dump_image.txt +++ b/doc/dump_image.txt @@ -10,23 +10,23 @@ dump image command :h3 [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 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 N = dump every this many timesteps :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 -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 - {atom} values = color diam = color and size of atoms - color = {none} or {type} or {element} or atom-attribute - diam = number or {type} or {element} or atom-attribute - number = numeric value for atom diameter (distance units) - {bond} values = color diam = color and width of bonds - color = {none} or {atom} or {type} - diam = number or {type} - numer = numeric value for bond diameter (distance units) +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 + {adiam} value = number = numeric value for atom diameter (distance units) + {atom} = yes/no = do or do not draw atoms + {bond} values = color width = color and width of bonds + color = {atom} or {type} + width = number or {atom} or {type} + number = numeric value for bond width (distance units) {size} values = width height = size of images width = width 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) {center} values = flag Cx Cy Cz = center point of image 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) {up} values = Ux Uy Uz = direction that is "up" in image 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 {shiny} value = factor = shinyness of spheres and cylinders factor = shinyness of spheres and cylinders from 0.0 to 1.0 - {ssao} value = yes/no = SSAO depth shading - yes/no = turn depth shading on/off :pre + {ssao} value = yes/no seed = SSAO depth shading + yes/no = turn depth shading on/off + seed = random # seed (positive integer) :pre :ule [Examples:] -dump myDump all image 100 dump.*.jpg :pre +dump myDump all image 100 dump.*.jpg type type :pre [Description:] @@ -111,21 +112,17 @@ correct ordering. :line -The kewords listed above control how the image is rendered. As listed -below, all of the keywords have defaults, most of which you will -likely not need to change. The "dump modify"_dump_modify.html also -has options specific to the dump image style, particularly for -assigning colors to atoms, bonds, and other image features. +The {color} and {diameter} settings determine the color and size of +atoms rendered in the image. They can be any atom attribute defined +for the "dump custom"_dump.html command, including {type} and +{element}. This includes per-atom quantities calculated by a +"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 - -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 +If {type} is specified for the {color} setting, then the color of each atom is determined by its atom type. By default the mapping of types to colors is as follows: @@ -139,25 +136,28 @@ type 6 = cyan :ul and repeats itself for types > 6. This mapping can be changed by the "dump_modify acolor"_dump_modify.html command. -If {element} is specified for the {color} value, then the color 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 associated with it, which is the same as the -colors used by the "AtomEye"_atomeye visualization package. +If {type} is specified for the {diameter} setting 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 {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) -An atom-attribute can also be used for the {color} value. Any -attribute listed on the "dump custom"_dump.html doc page can be used, -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. +If other atom attributes are used for the {color} or {diameter} +settings, they are interpreted in the following way. -The association of a per-atom value with a specific color is -determined by a "color map", which can be specified via the +If "vx", for example, is used as the {color} setting, then the color +of the atom will depend on the x-component of its velocity. The +association of a per-atom value with a specific color is determined by +a "color map", which can be specified via the "dump_modify"_dump_modify.html command. The basic idea is that the atom-attribute will be within a range of values, and every value within the range is mapped to a specific color. Depending on how the @@ -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 discretely so that the value of -3.2 is "orange". -The {diam} value can be a numeric value or {type} or {element} or an -atom-attribute. - -If a numeric value is specified, then all atoms will be drawn with -that diameter, e.g. 1.5, which is in distance units in whatever -"units"_units.html the input scripts uses, e.g. Angstroms. - -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. +If "vx", for example, is used as the {diameter} setting, then the atom +will be rendered using the x-component of its velocity as the +diameter. If the per-atom value <= 0.0, them the atom will not be +drawn. Note that finite-size spherical particles, as defined by +"atom_style sphere"_atom_style.html define a per-particle radius or +diameter, which can be used as the {diameter} setting. :line -The {bond} keyword determines the color and thickness or diameter of -bonds rendered in the image. If {none} is specified for the {color} -value (with any diam value), then no bonds are drawn. +The various kewords listed above control how the image is rendered. +As listed below, all of the keywords have defaults, most of which you +will likely not need to change. The "dump modify"_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 -in 2 halves, with the color of each half being the color of the atom -at that end of the bond. +:line + +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 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 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 -diameter, e.g. 1.0, which is in distance units in whatever -"units"_units.html the input script uses, e.g. Angstroms. +If a numeric value is specified, then all bonds will be drawn as +cylinders with that diameter, e.g. 1.0, which is in whatever distance +"units"_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 diameter 0.5. This mapping can be changed by the "dump_modify 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 (SSAO) model for depth shading. If {yes} is set, then atoms further -away from the viewer are darkened, which is perceived as depth. The -calculation of this effect can increase the cost of computing the -image by roughly 2x. If {no} is set, no depth shading is performed. +away from the viewer are darkened via a randomized process, which is +perceived as depth. The calculation of this effect can increase the +cost of computing the image by roughly 2x. If {no} is set, no depth +shading is performed. :line diff --git a/doc/dump_modify.html b/doc/dump_modify.html index de14830c56..11fea4f941 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -19,7 +19,7 @@
acolor args = type color
type = atom type or range of types (see below)
@@ -30,7 +30,7 @@
amap args = lo hi style N delta 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 = "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 @@
bdiam args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
- bgcolor arg = color
+ backcolor arg = color
color = name of color for background
boxcolor arg = color
color = name of color for box lines
@@ -109,9 +109,9 @@ parameters are relevant to all dump styles.
The acolor keyword applies only to the dump image style. It can
-be used with the dump image command, with its atom
-keyword, when its color setting is type, to set the color that atoms
-of each type will be drawn in the image.
+be used with the 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
@@ -124,23 +124,23 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive).
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
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.
The adiam keyword applies only to the dump image style. It can be
-used with the dump image command, with its atom
-keyword, when its diam 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 atomt types. The specified diam is the size in
-whatever distance units you are using, e.g. Angstroms.
+used with the 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 atomt
+types. The specified diam is the size in whatever distance
+units the input script is using, e.g. Angstroms.
@@ -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 dump_modify doc page.
+procedure.
There are many possible options for the color map, enabled by the
amap keyword. Here are the details.
@@ -167,8 +166,9 @@ which are explained on the dump_modify doc page
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 will the lower and/or
-upper bound will be calculated each time an image is drawn.
+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.
@@ -200,13 +200,13 @@ 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 colorname defined by the
+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 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
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".
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, including sub-ranges of
-values that 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.
+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
@@ -284,7 +284,7 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive).
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
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.
-The bgcolor keyword applies only to the dump image 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
+
The backcolor keyword applies only to the dump image 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.
@@ -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.
+
+
+
+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.
@@ -511,7 +526,7 @@ box size stored with the snapshot.
The style atom selects one or more atoms in a range of atom IDs. -The style type selects all the atoms in a range of types. The style +
The style atom selects all the atoms in a range of atom IDs. The +style type selects all the atoms in a range of types. The style 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 diff --git a/doc/set.txt b/doc/set.txt index f94edbf3f3..a768576f1d 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -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 compute subsequent forces or energy. -The style {atom} selects one or more atoms in a range of atom IDs. -The style {type} selects all the atoms in a range of types. The style +The style {atom} selects all the atoms in a range of atom IDs. The +style {type} selects all the atoms in a range of types. The style {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