6.2.7. GRAPHICS OPTION, [G]

next, previous Section / Table of Contents / Index [G] This option allows you to design the graphical/numerical screen (and PostScript file) output of a lattice section. It lets you choose different details of plots such as display mode (layer-by-layer, atom-by-atom, cell-by-cell), atom representations (points, circles, (shaded) balls, stereo duplication), layout (see Sec. 6.2.7.2), and colors. Further, you can define links (lines or cylindrical sticks) connecting atom pairs inside this option which serves to visualize bonds and neighbor relationships, see Sec. 6.2.7.1. The graphics option menu G reads ======= GRAPHICS OPTIONS =============================================== Graphs: [D]esign(gd) [S]tereo(st) [B]ackgr(nb) [P]alstart(np) [M]ode(gm) [C]link(nnc) [L]ayout(pl/xxl) c[T]abl [W]orkb {[X]plot} [?,]esc ================================================================== 29 == giving shorthand information about graphics options and parameters. In this menu parameter gd indicates the graphical representation of atoms in plots with gd = "Nx" for no plotting/listing (for testing only), = "Lx" for coordinate listing, = "Px" for atoms shown as points, = "Cx" for atoms shown as circles, = "Ax" for atoms shown as filled circles (areas), = "Rx" for atoms shown as red/blue stereo circles, = "Hx" for atoms shown as hard-shaded balls, = "Fx" for atoms shown as fuzzy-shaded balls, = "Dx" for atoms shown as dither-shaded balls, = "Gx" for atoms shown as glossy-shaded balls. The lower case character in parameter gd and parameter st refer to stereo duplication in plots where x = "m", st = "off" indicate mono views with one picture on the screen, = "s", st = "on" indicate stereo views showing two slightly different (reduced) pictures of the structure on the screen. Parameter nb in the above menu denotes the index of the color used to paint the background in plots while np gives the starting value of the color palette used to paint atoms. Parameter gm in the above menu shows the display mode where gm = "A" refers to atom-by-atom display mode, = "L" refers to layer-by-layer display mode, = "C" refers to cell-by-cell display mode (stacking of elementary cells). Parameter nnc in the above menu gives the number of constraints used to define links (lines or cylindrical sticks) connecting atom pairs to visualize bonds or neighbor relationships, see Sec. 6.2.7.1. Parameter pl in the above menu refers to painting and labelling of atoms where pl = "E-" paints atoms of different elements differently, no labels, = "EN" paints atoms of different elements differently, atom number labels, = "EE" paints atoms of different elements differently, element labels, = "L-" paints atoms of different layers differently, no labels, = "LN" paints atoms of different layers differently, atom number labels, = "LE" paints atoms of different layers differently, element labels, Parameter xxl in the above menu refers to the plot layout and reads "off" or any combination of the four characters "T", "B", "F", "-" where "T" shows if a title line is included, "B" shows if basis vectors are sketched in the plot, "F" shows if the lattice section is enclosed by a rectangular wire frame, "-" is used only as a filling character. All parameters shown in the graphics option menu are predefined internally by meaningful defaults which are, however, overwritten if an external structure file is loaded in a BALSAC/LATTICE session. > [D] selected from submenu G allows you to define how atoms are shown in subsequent plots or listings of a lattice section. The design submenu GD reads =================================================================== Design(gd): [N]one [L]ist [P]oint [C]ircle [A]rea [R]Bstereo balls: [H]ard [F]uzzy [D]ithered [G]lossy [S]tereodup(st) [X]plot [?,]esc ============================================================= 84 == where gd gives the present design code, see above, and parameter st reads "on" or "off" depending whether stereo duplication in plots is active or not, see option [S] below. Selecting from this menu option > > [N] will not show atoms by plots nor by listings but will calculate coordinates of all atoms of the lattice section if the execute option [X] is selected in the following. This option is meant only for testing purposes. > > [L] will list all atoms of the lattice section by Atom X Y Z Rad El/Nuc| Xp Yp Zp --------------------------------------------------------- 1) x y z rad nuc | xp yp zp ... if the execute option [X] is selected in the following. Here (x,y,z) are cartesian coordinates of each atom in real space, rad its atom radius, and nuc its element name and nuclear charge. Further, (xp,yp) are projected planar coordinates which can be directly used for a drawing, and zp denotes the height of the projected atom center above or below the drawing plane. Large listings (exceeding 18 atoms) will be interrupted and the prompt ** Press [C], L-click ([/], B-click) to continue; [,], R-click to escape ** allows you to continue (select [C], in single atom mode select [/], see Sec. 6.2.9) or finish listing (select [,]). This option value is useful if BALSAC runs on a PC or workstation without graphics adapter. It can also be used in exploratory studies when the actual number of atoms in a plot has to be selected and a graphical representation would look too busy or confusing. > > [P] will represent atoms of the lattice section by DOTS (very small circles) in subsequent plots. > > [C] will represent atoms of the lattice section by CIRCLES in subsequent plots. > > [A] will represent atoms of the lattice section by FILLED CIRCLES (overlapping areas) in subsequent plots. > > [R] will represent atoms of the lattice section by RED/BLUE STEREO circles in subsequent plots. Each atom will be shown by two circles, a left (blue) circle and a right (red) circle, where the distance between the circles increases with decreasing distance from the viewer (depending on the perspective used, see Sec. 6.2.6). This rather fast plot mode allows you to get a true 3-dimensional impression of the lattice section when blue/red stereo filter glasses are used. The actual amount of stereo distortion may be modified in the basic parameter option, see Sec. 6.2.15. Note that any stereo picture produced by BALSAC yields meaningful results only for non-zero values of the perspective parameter persp, see Sec. 6.2.6. > > [H] will represent atoms of the lattice section by HARD-SHADED BALLS in subsequent plots. Shading is achieved by subdividing the visible ball area in two parts displayed by dark and light tones of paint color n as defined in the initialization file, see Secs. 6.2.15, 6.4.10. > > [F] will represent atoms of the lattice section by FUZZY-SHADED BALLS in subsequent plots. Continuous shading is achieved by a statistical pattern using light and dark tones of paint color n as defined in the initialization file, see Secs. 6.2.15, 6.4.10. > > [D] will represent atoms of the lattice section by DITHER-SHADED BALLS in subsequent plots. Continuous shading is achieved by a 2x2 tri-level dither pattern using black, light, and dark tones of paint color n as defined in the initialization file, see Secs. 6.2.15, 6.4.10. > > [G] will represent atoms of the lattice section by GLOSSY-SHADED BALLS in subsequent plots. Continuous shading is achieved by using diffuse background color, Lambert shading and specular reflection with the relative contributions defined in the initialization file, see Secs. 5.4, 6.2.15, 6.4.10. This option is of limited quality in the DOS version of BALSAC due to the limited number of different colors available with VGA adapters. If BALSAC is run in color graphics mode atoms will be plotted with different color depending on the color mode option (see mode option [M] below). For circle and ball radii respective atom radii are used except for red/blue stereo display, option [R], where circle radii are given by respective atom radii reduced by a factor 0.4. Shading of atoms represented by balls is used to enhance the 3-dimensional impression. The actual amount of shading and the direction of incident light may be modified in the basic parameter option, see Sec. 6.2.15. While fuzzy, dithered, and glossy balls can give a more natural view of a lattice section they can be rather time consuming and are not recommended in exploratory studies of a structure. After any of the above atom representations in plots/listings has been selected BALSAC returns to submenu G. > > [S] selected from submenu GD allows you to switch between mono view and full color stereo view where the present setting is indicated by parameter st in submenu GD (st = "off" for mono views, = "on" for stereo views). While a mono view displays the lattice section by one picture on the screen (or in a PostScript print output) the full color stereo view shows two pictures. The pictures are reduced by 50% in size with respect to their mono equivalents, are horizontally displaced and slightly different in their projection geometry reflecting the eye and viewer's distance (freely adjustable inside the parameter option, see stereo parameters pu, deye of Sec. 6.2.15.). This full color stereo mode allows you to get a 3-dimensional impression of the lattice section using optical stereo glasses. Note that any stereo picture produced by BALSAC yields meaningful results only for non-zero values of the perspective parameter persp, see Sec. 6.2.6. After some exercise the full color stereo impression can also be obtained without optical glasses. Try the following: Look exactly at the center of the screen (with the two separate stereo pictures). Then put one finger to the screen center and move it slowly towards your eyes focusing at the finger tip. This will generate the illusion of seeing 4 (defocussed and overlapping) pictures on the screen. Stop moving your finger when two of the pictures overlap in the center giving you the impression of seeing 3 pictures. Try to concentrate on the center picture and after some time (depending on talent and practice) it will be focussed and stereo-type (while the two pictures to the left and right remain defocussed). Note that this stereo viewing requires a negative value for the distance shift between the two pictures while positive shift values are needed if optical stereo glasses are used, see also Sec. 6.2.15. NOTE that the kind of cross-eyed viewing required to obtain a stereo impression without optical glasses may strain your eyes! No responsibility can be taken by the author of BALSAC. > > [X] selected from submenu GD plots the lattice section (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the graphics option, see Sec. 6.2.7. > > [,] selected from submenu GD returns immediately to the graphics option menu G. Note that all graphics screen output requires a VGA/EGA/CGA graphics adapter working correctly on your PC (BALSAC DOS version) or an Xwindows color graphics output device (X-terminal or workstation, BALSAC Unix version). Asking for graphics output on a PC without graphics facilities may lead to unpredictable results. If BALSAC (Unix version) is run on a terminal (workstation) without Xwindows capabilities processing graphics with the execute option [X] leads to an error message ERROR: can't open display {ddd:0.0} where ddd:0.0 is the name of the presently defined output device which is followed by the prompt [C]alculate atom centers [?,]esc Selecting [C] from this menu will calculate and list all atoms of the section analogous to option [L] above whereas selecting [,] will directly move to the main option menu. Calculating atom centers is essential for storing atom coordinates on output files, see Secs. 6.2.8, 6.2.16, 6.3.6, 6.3.14. > [S] selected from submenu G allows you to switch between mono view and full color stereo view where the present setting is indicated by parameter st in submenu G (st = "off" for mono views, = "on" for stereo views). This option is identical to option [S] of submenu GD described in detail above. > [B] selected from submenu G allows you to define the background color used in subsequent plots of the lattice section. The prompt Input background color NB ( nbold: 0 - nctot) : asks for a color code number nb within the range [0,nctot] where nbold gives the present value. The numbers refer to entries of the internal color table determined by the initialization file and generated when BALSAC is started, see Sec. 5.4. Possible colors can be inspected by the color table display, option [T] of submenu G, see below. The background color will be defaulted to nb = 0 ( = black) in red/blue stereo mode and for monochrome mode, see below. Background colors other than black may hide lines / circles / balls painted with the same color. Note that the graphic analysis option offers a background color selection which is much more intuitive and faster, see Sec. 6.3.12. > [P] selected from submenu G allows you to set the starting point inside the color palette used in atom painting. The color palette consists of entries np(i), i=1...nptot pointing each at a paint color j (np(i) = j). This determines a basic sequence of paint colors which are used to discriminate between atoms of different layers or elements. The present option allows you to define the starting point npst inside the palette (of nptot entries) which will be used to choose the first color np(npst) for painting the first layer or atom type (element) to be plotted. Subsequent layers/elements use colors according to the palette sequence np(npst+1), np(npst+2),... The prompt Input color palette start NS ( npold: 0, 1 - nptot) : asks for a number defining the start value npst of the color palette used in subsequent plots where npold gives the present value. Here a value npst = 0 denotes black/white graphics while npst within the range [1,nptot] results in color graphics referring to the entry sequence of the color palette. The complete color palette can be inspected by the color table display, option [T] of submenu G, see below. The palette sequence of colors for subsequent layers/elements is continued periodically if the number of layers/elements exceeds the palette size nptot. The color palette can be redefined interactively and stored on separate initialization files using the basic parameter option, see Sec. 6.2.15.1. It is also redefined when atom colors are assigned in the graphic analysis, see Secs. 6.2.14.2, 6.3.12.2. > [M] selected from submenu G allows you to set the display mode used in plots of the lattice section. This offers different ways of watching the lattice building process. The mode submenu GM reads =================================================================== Mode (gm): [L]ayer-by-layer [A]tom-by-atom [C]ells [X]plot [?,]esc ============================================================= 83 == where gm shows the present value of the display mode. > > [L] selected from submenu GM sets layer-by-layer display mode where the lattice section will be built one lattice plane (layer) after the other. In interactive mode BALSAC stops after a layer is completed and shows ** Press [C], L-click ([/], B-click) to continue; [,], R-click to escape ** at the bottom of the screen (graphics window). This allows you to continue with the next layer (select [C], in single atom mode select [/], see Sec. 6.2.9) or finish the plot (select [,]). Note that in layer-by-layer display mode each layer must not contain more than namax atoms (namax = 2001 for DOS, = 8000 for Unix). Otherwise, only namax atoms per layer will be displayed resulting in incomplete layers. Since the number of layers in a lattice section is not limited by BALSAC the total number of atoms displayed in layer-by-layer mode may be much larger than nmax. In layer-by-layer display mode the atoms of each layer are sorted with respect to their distance from the viewer to yield a correct perspective view but adjacent layers are NOT considered in this sorting process. This may lead to erroneously overlapping atom spheres, in particular, if viewing angles theta > 90 are used. Therefore, selecting layer-by-layer display mode with theta > 90 will lead to a warning WARNING: Layer-by-layer display mode, Theta = theta may give incorrect views, use Theta <= 90 or atom-by-atom mode In layer-by-layer display mode only atoms of the layer displayed last are accessible in the graphic analysis option, see Sec. 6.2.14.2. > > [A] selected from submenu GM sets atom-by-atom display mode where the lattice section will be built as a whole depending on the viewing angle. Here all atoms of the lattice section are sorted with respect to their distance from the viewer and then displayed in the order of decreasing distance. This enhances the 3-dimensional perspective impression. > > [C] selected from submenu GM sets cell-by-cell display mode where the lattice section will be built as in atom-by-atom display mode. However, in the section definition, see 6.2.4, the layer stacking has a different meaning. Here the number n3 of layers to be included in the lattice section refers to layers of complete elementary cells (containing more than one atom in non-primitive lattices) rather than to inequivalent lattice planes. This display mode guarantees that molecules included in the elementary cell will not be truncated at the bottom or top of the lattice section. They may, however, be cut off at the four sides of the block. Here the initial layer index ninit, see 6.2.4, has no meaning and layer restructuring, see Sec. 6.2.5, is ignored. > > [X] selected from submenu GM plots the lattice section (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the graphics option, see Sec. 6.2.7. > > [,] selected from submenu GM returns immediately to the graphics option menu G. > [C] selected from submenu G allows you to define links connecting atoms (represented in plots by straight lines or cylindrical sticks) which can be used to visualize bonds or neighbor relationships in the lattice section. Further details are given in Sec. 6.2.7.1. > [L] selected from submenu G allows you to define additional layout parameters (framing, painting, labelling, etc.) used in screen plots and for PostScript file output. Further details are given in Sec. 6.2.7.2. > [T] selected from submenu G displays a color test table (in a separate graphics window, Unix) showing all color definitions together with color numbers available inside BALSAC. The colors are described in the initialization file and generated when BALSAC is started, see Sec. 5.4. The first line from the top of the table shows blocks of the base colors together with their names where the DOS/VGA version of BALSAC lists four colors defining "black", "white", "stereo red", "stereo blue" by black white (st)red (st)blue and the Unix/X.11 version lists eight colors defining "black", "white", "background", "text", "bonds", "stereo red", "stereo blue", "stereo white" by blck wht bckg txt bnd srd sbl swt Then the dark and light tones of all paint colors in the sequence of the palette definition are shown together with a line colors: palette= nptot, total= nctot where nptot is the number of entries in the color palette and nctot is the total number of RGB colors defined at present. Next for each of the ncolb paint colors the sequence of nsh tones, see Sec. 5.4, is displayed by a row of blocks going from darkest to lightest tones. The line to the right of each block sequence reads j ( def.dark(j) , def.light(j) ) ns(j)+1 - ns(j)+nsh where j is the paint color index (to be used in the palette for painting (shaded) balls), def.dark(j) and def.light(j) are color table entries of the default dark and light tones, and ns(j)+1 denotes the darkest, ns(j)+nsh the lightest tone of paint color j. In addition the two default color tones are marked by crossing lines in the respective color blocks (def.dark = white lines, def.light = black lines). Pressing [blank] clears the window and returns to the previous menu. The Unix/X.11 version of BALSAC shows in addition glossy-shaded balls next to each of the paint color rows using the respective color tones and demonstrating the incident light direction as well as diffuse, Lambert shading, and specular reflection contributions. > [W] selected from submenu G moves to the color/shading workbench switching to graphics mode (DOS) or opening a graphics window (Unix). This allows you to change all basic and paint colors as well as ball shading angles in a very intuitive way using the mouse or a graphics pointer. Further details are given in Sec. 6.2.15.2. > [X] selected from submenu G plots the lattice section (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the present graphics option. > [,] selected from submenu G returns immediately to the BALSAC/LATTICE main option menu. Note that the graphics option menu G is the last menu which requires input if a lattice section is built from scratch. If BALSAC/LATTICE is started with a structure input file the above graphics parameters are given in compressed and number coded form in the file. Here the display mode, atom representation, and mono/stereo view option are combined in one compound index M where M = SF * (10 * K + L) with SF = 1 for mono viewing (option [S]), = -1 for stereo duplication (option [S]). K = 0 for layer-by-layer display mode (option [L]), = 1 for atom-by-atom display mode (option [A]), = 2 for cell-by-cell-display mode (option [C]). L = 0 for no plot/listing output (testing purposes, option [N]), = 1 for atom coordinate listing, no graphics (option [L]), = 2 for atoms plotted as color dots (small circles, option [P]), = 3 for atoms plotted as color circles (option [C]), = 4 for atoms plotted as color filled circles (option [A]), = 5 for atoms plotted as red/blue stereo circles (option [R]), = 6 for atoms plotted as hard-shaded balls (option [H]), = 7 for atoms plotted as fuzzy-shaded balls (option [F]), = 8 for atoms plotted as dither-shaded balls (option [D]), = 9 for atoms plotted as glossy-shaded balls (option [G]). Further, the background color index and the starting value of the color palette used to paint atoms are combined in one compound index N where N = 100 * nb + npst where nb denotes the background color and npst denotes the palette start, see above. next, previous Section / Table of Contents / Index