"SPPARKS WWW Site"_sws - "SPPARKS Documentation"_sd - "SPPARKS Commands"_sc :c :link(sws,http://www.cs.sandia.gov/~sjplimp/spparks.html) :link(sd,Manual.html) :link(sc,Section_commands.html#comm) :line dump_modify command :h3 [Syntax:] dump_modify dump-ID keyword values ... :pre dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l keyword = {backcolor} or {boundcolor} or {boxcolor} or {color} or {delay} or {delta} or {flush} or {logfreq} or {loglinfreq} or {pad} or {region} or {scolor} or {sdiam} or {smap} or {thresh} :l {backcolor} arg = color color = name of color for background {boundcolor} arg = color color = name of color for boundaries between sites {boxcolor} arg = color color = name of color for box lines {color} args = name R G B name = name of color R,G,B = red/green/blue numeric values from 0.0 to 1.0 {delay} value = tdelay tdelay = delay dump until at least this time (seconds) {delta} arg = dt dt = time increment between dumps (seconds) {flush} arg = {yes} or {no} {logfreq} or {loglinfreq} values = N factor N = number of repetitions per interval factor = scale factor between intervals {pad} arg = Nchar = # of characters to convert timestep to {region} arg = region-ID or "none" {scolor} args = I color I = integer value or range of values (see below) color = name of color or color1/color2/... or {random} {sdiam} args = I diam I = integer value or range of values (see below) diam = diameter of sites of that value {smap} args = lo hi style delta N entry1 entry2 ... entryN lo = number or {min} = lower bound of range of color map hi = number or {max} = upper bound of range of color map style = 2 letters = "c" or "d" or "s" plus "a" or "f" "c" for continuous "d" for discrete "s" for sequential "a" for absolute "f" for fractional delta = binsize (only used for style "s", otherwise ignored) binsize = range is divided into bins of this width N = # of subsequent entries entry = value color (for continuous style) value = number or {min} or {max} = single value within range color = name of color used for that value entry = lo hi color (for discrete style) lo/hi = number or {min} or {max} = lower/upper bound of subset of range color = name of color used for that subset of values entry = color (for sequential style) color = name of color used for a bin of values {thresh} args = attribute operation value attribute = same fields (id,lattice,x,etc) used by "dump"_dump.html command operation = "<" or "<=" or ">" or ">=" or "==" or "!=" value = numeric value to compare to these 3 args can be replaced by the word "none" to turn off thresholding :pre :ule [Examples:] dump_modify 1 delay 30.0 dump_modify 1 loglinfreq 7 10.0 delay 100.0 flush yes dump_modify mine thresh energy > 0.0 thresh id <= 1000 :pre [Description:] Modify the parameters of a previously defined dump command. Not all parameters are relevant to both the {text} and {image} dump styles. :line 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. :line The {boundcolor} keyword applies only to the dump {image} style. It sets the color used to draw boundaries between sites, each of which is a set of 4 cylinders, as described in the "dump image"_dump_image.html doc page. The color name can be any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option. The drawing of boundaries between neighboring sites is enabled by the {boundary} keyword of the "dump image"_dump_image.html command. :line The {boxcolor} keyword applies only to the dump {image} style. It sets the color of the simulation box drawn around the sites 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 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 The {delay} keyword will suppress output until {tdelay} time has elapsed. :line The {delta} keyword will suppress output until {tdelay} time has elapsed. :line The {flush} option determines whether a flush operation in invoked after a dump snapshot is written to the dump file. A flush insures the output in that file is current (no buffering by the OS), even if SPPARKS halts before the simulation completes. The {flush} option is only relevant to the "dump text"_dump.html style. :line The {logfreq} and {loglinfreq} keywords will produce output at progressively larger intervals during the course of a simulation. There will be {N} outputs per interval where the size of each interval is initially {delta} and then scales up by {factor} each time. See the "stats"_stats.html command for more information on how the output times are specified. If {N} is specified as 0, then this will turn off logarithmic output, and revert to regular output every {delta} seconds. :line The {pad} keyword only applies when the dump filename is specified with a wildcard "*" character which becomes the timestep. If {pad} is 0, which is the default, the timestep is converted into a string of unpadded length, e.g. 100 or 12000 or 2000000. When {pad} is specified with {Nchar} > 0, the string is padded with leading zeroes so they are all the same length = {Nchar}. For example, pad 7 would yield 0000100, 0012000, 2000000. This can be useful so that post-processing programs can easily read the files in ascending timestep order. :line The {region} keyword allows sub-selection of lattice sites to output. If specified, only sites in the region will be written to the dump file or included in the image. Only one region can be applied as a filter (the last one specified). See the "region"_region.html command for more details. Note that a region can be defined as the "inside" or "outside" of a geometric shape, and it can be the "union" or "intersection" of a series of simpler regions. :line The {scolor} keyword applies only to the dump {image} style. It can be used with the "dump image"_dump_image.html command, when its site color setting is an integer attribute, and a {crange} setting from {lo} to {hi} has been specified to set the color associated with each integer value. The specified {I} value should be an integer from {lo} to {hi} inclusive. A wildcard asterisk can be used in place of or in conjunction with the {type} argument to specify a range of values. This takes the form "*" or "*n" or "n*" or "m*n". An asterisk with no numeric values means all values from {lo} to {hi}. A leading asterisk means all values from {lo} to n (inclusive). A trailing asterisk means all values from n to {hi} (inclusive). A middle asterisk means all values from m to n (inclusive). The specified {color} can be a single color which is any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option. Or it can be two or more colors separated by a "/" character, e.g. red/green/blue. In the former case, that color is assigned to all the specified integer values. In the latter case, the list of colors are assigned in a round-robin fashion to each of the specified integer values. The specified {color} can also be the word {random}. In this case, random red/blue/green color values, each from 0.0 to 1.0, are generated for each {I} value. This is a convenient way to assign a large number of random colors, without having to list them explicitly by name. :line The {sdiam} keyword applies only to the dump {image} style. It can be used with the "dump image"_dump_image.html command, when its site diameter setting is an integer attribute, and a {drange} setting from {lo} to {hi} has been specified to set the diameter associated with each integer value. The specified {I} value should be an integer from {lo} to {hi}. As with the {scolor} keyword, a wildcard asterisk can be used as part of the {I} argument to specify a range of values. :line The {smap} keyword applies only to the dump {image} style. It can be used with the "dump image"_dump_image.html command, when its site color setting is a floating point attribute, to setup a color map. The color map is used to assign a specific RGB (red/green/blue) color value to an individual site when it is drawn, based on the atom's attribute, which is a numeric value, e.g. its x coordinate, if the attribute "x" was specified. The basic idea of a color map is that the site-attribute will be within a range of values, and that range is associated with a series of colors (e.g. red, blue, green). An sites's specific value (x = -3.2) can then mapped to the series of colors (e.g. halfway between red and blue), and a specific color is determined via an interpolation procedure. There are many possible options for the color map, enabled by the {smap} keyword. Here are the details. The {lo} and {hi} settings determine the range of values allowed for the site attribute. If numeric values are used for {lo} and/or {hi}, then values that are lower/higher than lo/hi are set to either {lo} or {hi}. I.e. the range is static. If {lo} is specified as {min} or {hi} as {max} then the range is dynamic, and the lower and/or upper bound will be calculated each time an image is drawn, based on the set of sites being visualized. The {style} setting is two letters, such as "ca". The first letter is either "c" for continuous, "d" for discrete, or "s" for sequential. The second letter is either "a" for absolute, or "f" for fractional. A continuous color map is one in which the color changes continuously from value to value within the range. A discrete color map is one in which discrete colors are assigned to sub-ranges of values within the range. A sequential color map is one in which discrete colors are assigned to a sequence of sub-ranges of values covering the entire range. An absolute color map is one in which the values to which colors are assigned are specified explicitly as values within the range. A fractional color map is one in which the values to which colors are assigned are specified as a fractional portion of the range. For example if the range is from -10.0 to 10.0, and the color red is to be assigned to atoms with a value of 5.0, then for an absolute color map the number 5.0 would be used. But for a fractional map, the number 0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. The {delta} setting is only specified if the style is sequential. It specifies the bin size to use within the range for assigning consecutive colors to. For example, if the range is from -10.0 to 10.0 and a {delta} of 1.0 is used, then 20 colors will be assigned to the range. The first will be from -10.0 <= color1 < -9.0, then 2nd from -9.0 <= color2 < -8.0, etc. The {N} setting is how many entries follow. The format of the entries depends on whether the color map style is continuous, discrete or sequential. In all cases the {color} setting can be any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option. For continuous color maps, each entry has a {value} and a {color}. The {value} is either a number within the range of values or {min} or {max}. The {value} of the first entry must be {min} and the {value} of the last entry must be {max}. Any entries in between must have increasing values. Note that numeric values can be specified either as absolute numbers or as fractions (0.0 to 1.0) of the range, depending on the "a" or "f" in the style setting for the color map. Here is how the entries are used to determine the color of an individual site, given the value X of its site attribute. X will fall between 2 of the entry values. The color of the site is linearly interpolated (in each of the RGB values) between the 2 colors associated with those entries. For example, if X = -5.0 and the 2 surrounding entries are "red" at -10.0 and "blue" at 0.0, then the site's color will be halfway between "red" and "blue", which happens to be "purple". For discrete color maps, each entry has a {lo} and {hi} value and a {color}. The {lo} and {hi} settings are either numbers within the range of values or {lo} can be {min} or {hi} can be {max}. The {lo} and {hi} settings of the last entry must be {min} and {max}. Other entries can have any {lo} and {hi} values and the sub-ranges of different values can overlap. Note that numeric {lo} and {hi} values can be specified either as absolute numbers or as fractions (0.0 to 1.0) of the range, depending on the "a" or "f" in the style setting for the color map. Here is how the entries are used to determine the color of an individual site, given the value X of its site attribute. The entries are scanned from first to last. The first time that {lo} <= X <= {hi}, X is assigned the color associated with that entry. You can think of the last entry as assigning a default color (since it will always be matched by X), and the earlier entries as colors that override the default. Also note that no interpolation of a color RGB is done. All sites will be drawn with one of the colors in the list of entries. For sequential color maps, each entry has only a {color}. Here is how the entries are used to determine the color of an individual site, given the value X of its site attribute. The range is partitioned into N bins of width {binsize}. Thus X will fall in a specific bin from 1 to N, say the Mth bin. If it falls on a boundary between 2 bins, it is considered to be in the higher of the 2 bins. Each bin is assigned a color from the E entries. If E < N, then the colors are repeated. For example if 2 entries with colors red and green are specified, then the odd numbered bins will be red and the even bins green. The color of the site is the color of its bin. Note that the sequential color map is really a shorthand way of defining a discrete color map without having to specify where all the bin boundaries are. :line The {thresh} keyword allows sub-selection of lattice sites to output. Multiple thresholds can be specified. Specifying "none" turns off all threshold criteria. If thresholds are specified, only sites whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible attributes that can be tested for are the same as the fields that can be specified in the "dump"_dump.html command. Note that different attributes can be output by the dump command than are used as threshold criteria by the dump_modify command. E.g. you can output the coordinates and propensity of sites whose energy is above some threshold. [Restrictions:] This command can only be used as part of the lattice-based applications. See the "app_style"_app_style.html command for further details. [Related commands:] "dump"_dump.html, "dump image"_dump_image.html [Default:] The option defaults are backcolor = black boundcolor = white boxcolor = yellow color = 140 color names are pre-defined as listed below delay = 0.0 delta = value used in the "dump"_dump.html command flush = yes logfreq = off loglinfreq = off pad = 0 region = none scolor = * red/green/blue/yellow/aqua/cyan sdiam = * 1.0 smap = min max cf 2 min blue max red thresh = none :ul :line These are the 140 colors that SPPARKS pre-defines for use with the "dump image"_dump_image.html and dump_modify commands. Additional colors can be defined with the dump_modify color command. The 3 numbers listed for each name are the RGB (red/green/blue) values. Divide each value by 255 to get the equivalent 0.0 to 1.0 value. aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 | beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 | blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 | chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 | cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 | darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 | darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 | darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 | dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 | fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 | gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 | indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 | lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 | lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 | lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 | lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 | maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 | mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 | midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 | navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 | orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 | palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 | plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 | royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 | seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 | slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 | teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 | wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 :tb(c=5,s=|)