3d visualization via Raster3d program.
The raster tool is a wrapper on the Raster3d visualization program. Raster3d is open source software and runs on many platforms.
The raster constructor takes a data object containing atom or mesh snapshots as an argument (dump, data, cdata, mdump).
The show() method runs Raster3d on the selected atoms or triangles of snapshot N and displays the resulting image stored as image.png. The all() method loops thru all selected snapshots and runs Raster3d on each one. The resulting image files are saved to image0000.png, image0001.png, etc. The prefix "image" can be changed via the file setting.
The bg(), size(), rotate(), trans(), zoom(), box(), label(), and nolabel() methods control various aspects of the images produced. Without the trans() and zoom() settings, the Raster3d image should roughly fill the window and be centered.
Additional movie effects can be produced using the pan() and select() methods. The pan() method specifies an initial and final viewpoint that is applied to the images produced by the all() method. For intermediate images, the view parameters will be interpolated between their initial and final values. The pan() method can thus be used to rotate a single image or fly-by the simulation as it animates. The select() method performs additional atom selection for each image of the all() sequence. An image-dependent %g variable can be used in the select() string. The select() method can thus be used to slice thru the data set.
The acol(), arad(), bcol(), brad(), and tcol() methods change attributes of the atoms, bonds, and triangles displayed. Each atom or bond returned from the data object has an integer "type" from 1 to N. The type is used to index into a list of RGB colors or radii for atoms and bond thickness. The adef(), bdef(), and tdef() methods setup default mappings of types to colors/radii. The other methods enable specific assignments to be made. The interpolation option (e.g. many types assigned to a few colors), enables a smooth rainbow of colors to be assigned to a range of types. Note that the dump tool allows any vector to be returned as an atom "type" via its atype setting. Thus displayed colors can be keyed to atom velocity or other properties.
Colors are specified with a string, e.g. "red". There are 140 pre-defined colors from this WWW page which can be examined by importing the "colors" variable from "vizinfo". New colors can be defined by assigning a nickname of your choice to an RGB triplet, as described below.
r = raster(d) create Raster3d wrapper for data in d
d = atom snapshot object (dump, data)
r.bg("black") set background color (def = "black") r.size(N) set image size to NxN r.size(N,M) set image size to NxM r.rotate(60,135) view from z theta and azimuthal phi (def = 60,30) r.shift(x,y) translate by x,y pixels in view window (def = 0,0) r.zoom(0.5) scale image by factor (def = 1) r.box(0/1/2) 0/1/2 = none/variable/fixed box r.box(0/1/2,"green") set box color r.box(0/1/2,"red",4) set box edge thickness r.file = "image" file prefix for created images (def = "image")
r.show(N) show image of snapshot at timestep N
r.all() make images of all selected snapshots r.all(P) images of all, start file label at P r.all(N,M,P) make M images of snapshot N, start label at P
r.pan(60,135,1.0,40,135,1.5) pan during all() operation r.pan() no pan during all() (default)
args = z theta, azimuthal phi, zoom factor at beginning and end values at each step are interpolated between beginning and end values
r.select = "$x > %g*3.0" string to pass to d.aselect.test() during all() r.select = "" no extra aselect (default)
%g varies from 0.0 to 1.0 from beginning to end of all()
r.label(x,y,"h",size,"red","This is a label") add label to each image r.nolabel() delete all labels
x,y coords = -0.5 to 0.5, "h" or "t" for Helvetica or Times font size = fontsize (e.g. 10), "red" = color of text
r.acol(2,"green") set atom colors by atom type (1-N) r.acol([2,4],["red","blue"]) 1st arg = one type or list of types r.acol(0,"blue") 2nd arg = one color or list of colors r.acol(range(20),["red","blue"]) if list lengths unequal, interpolate r.acol(range(10),"loop") assign colors in loop, randomly ordered
if 1st arg is 0, set all types to 2nd arg if list of types has a 0 (e.g. range(10)), +1 is added to each value interpolate means colors blend smoothly from one value to the next
r.arad([1,2],[0.5,0.3]) set atom radii, same rules as acol()
r.bcol() set bond color, same args as acol() r.brad() set bond thickness, same args as arad()
r.tcol() set triangle color, same args as acol() r.tfill() set triangle fill, 0 fill, 1 line, 2 both
r.lcol() set line color, same args as acol() r.lrad() set line thickness, same args as arad()
r.adef() set atom/bond/tri/line properties to default r.bdef() default = "loop" for colors, 0.45 for radii r.tdef() default = 0.25 for bond/line thickness r.ldef() default = 0 fill
by default 100 types are assigned if atom/bond/tri/line has type > # defined properties, is an error
from vizinfo import colors access color list print colors list defined color names and RGB values colors["nickname"] = [R,G,B] set new RGB values from 0 to 255
140 pre-defined colors: red, green, blue, purple, yellow, black, white, etc
dump, gl, rasmol, svg
The Raster3d render and label3d programs.