6.3.6. FILE OUTPUT OPTION, [O]

next, previous Section / Table of Contents / Index [O] This option allows you to save all structure and graphics information of the present BALSAC/CLUSTER session on output files. These files can be used as input to subsequent BALSAC/CLUSTER runs or with other analysis or visualization software depending on the output format. Available formats are discussed below and in Secs. 6.4.2-6 and include encapsulated (color) PostScript file output for high quality graphics prints on PostScript laser printers. The present option is in many details identical to the file output option of BALSAC/LATTICE sessions but offers a smaller selection of output formats, see Sec. 6.2.8. The file output menu O reads ========== FILE STORE OPTIONS ================================ Latest input = {inputfilename} [F]ilesave [Q]uicksave [I]nit(fin) l[O]go(flg) [?,]esc ======================================================== 27 == where the present settings of the initialization and logo option flags, fin and flg (reading "on" or "off", see below), are shown. The line "Latest ..." gives the name of the latest input file (enclosed by "{...}") read by balsac or shows "{}" if no input file has been used so far. > [F] selected from submenu O allows you to give a name of an external file which will be used for subsequent output. The prompt Output file name ("-"=esc): asks for a character string fname (up to 72 characters) defining the file name, e.g. "out.new". Note that BALSAC does not check and warn you if a file name denotes an existing file where there is a risk of overwriting data by BALSAC output. With the DOS version of BALSAC using "PRN" as file name will send the output directly to the default printer connected to the PC without storing in a file. Note that PostScript output format is meaningful only for true PostScript laser printers and other printers may produce lots of useless output. The file name input is confirmed by Open: fname after which the output file fname is opened and the file format menu OF reading ================================================================== Format: [P]lt [L]at sch[K]l [D]pdb [F]xyz [G]ps [C]olps {[R]bin} [I]nit(fin) l[O]go(flg) [?,]esc ============================================================ 28 == allows you to select the format of the output file (and change the initialization and logo option flags). > > [P] selected from submenu OF saves all structure and graphics data of the present BALSAC/CLUSTER session using PLOT3D format, see Sec. 6.4.3. This is confirmed by Saving data on file : PLOT3D format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. Output files of PLOT3D format can be used as input to subsequent BALSAC/CLUSTER sessions as well as to PLOT3D ((C) Copyright 1991-5 K. Hermann), a PC based analysis and visualization tool for non-periodic structures (clusters, molecules, disordered systems), see Sec. 1.3. > > [L] selected from submenu OF saves all structure and graphics data of the present BALSAC/CLUSTER session using standard LATUSE format (Cards 1-18), see Sec. 6.4.2. This is confirmed by Saving data on file : LATUSE format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. Here the atoms of the cluster are interpreted as forming the crystallographic unit cell of an orthorhombic lattice with lattice vectors (in cartesian coordinates) R1 = ( xtot * 1.5, 0.0 , 0.0 ) R2 = ( 0.0 , ytot * 1.5, 0.0 ) R3 = ( 0.0 , 0.0, ztot * 1.5 ) where xtot, ytot, ztot are the lengths of the rectangular block containing all cluster atoms. The lattice periodicity (as well as the atom basis) may be changed after transfer inside the BALSAC/LATTICE session with the lattice update option, see Sec. 6.2.1.2. If the total number nct of cluster atoms exceeds the maximum number nbmax of lattice basis vectors of a BALSAC/LATTICE session (nbmax = 201 at present) only nbmax atoms are used to build the elementary cell of the lattice. Output files of LATUSE format can be used as input to subsequent BALSAC/LATTICE sessions as well as to LATUSE ((C) Copyright 1991-5 K. Hermann), a PC based analysis and visualization tool for periodic structures and surfaces, see Sec. 1.3. > > [K] selected from submenu OF saves all structure data of the present BALSAC/CLUSTER session using SCHAKAL format, see Sec. 6.4.5. This is confirmed by Saving data on file : SCHAKAL format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. Output files of SCHAKAL format can be used as input to SCHAKAL ((C) Copyright 1992 E. Keller), a widely used crystal visualization tool. BALSAC uses only a restricted SCHAKAL format as described in Sec. 6.4.5. This format cannot account for all structural features available with SCHAKAL. For further details consult the SCHAKAL documentation. > > [D] selected from submenu OF saves all structure data of the present BALSAC/CLUSTER session using PDB format, see Sec. 6.4.8. This is confirmed by Saving data on file : PDB format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. Output files of PDB format (last draft version 2.1, October 25, 1996, (C) Brookhaven National Laboratory) can be used as input to many different molecular visualization and database packages, such as Rasmol, WebLab Viewer, and others. BALSAC uses only a restricted PDB format as described in Sec. 6.4.8. > > [F] selected from submenu OF saves all structure data of the present BALSAC/CLUSTER session using XYZ format, see Sec. 6.4.9. This is confirmed by Saving data on file : XYZ format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. Output files of XYZ format ((C) Research Equipment Inc. 1991) can be used as input to many different molecular visualization packages, such as Xmol. BALSAC uses only a restricted XYZ format as described in Sec. 6.4.9. > > [G]/[C] selected from submenu OF stores the complete graphics information of the present BALSAC/CLUSTER session using (encapsulated) gray scale ([G]) or color ([C]) PostScript format, see Sec. 6.4.6. If fuzzy-, dither-, or glossy-shaded balls are used to represent atoms BALSAC prompts No. of PostScript tones (1-50) : asking for the number of tones nshps < 50 to be used for shading in the PostScript output (see Sec. 5.4). The output is confirmed by Saving data on file : Gray scale PostScript format File output completed ** Press [C], L-click to continue ** (DOS only) or Saving data on file : Color PostScript format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its CLUSTER main option menu. PostScript files can be printed on PostScript laser printers or typesetting systems yielding high quality graphics prints. On B/W PostScript printers colors and shading are simulated by gray levels using fixed dithering. Since PostScript files are ASCII-type they can be easily modified outside BALSAC with text editors to improve the print quality even further, see Secs. 6.4.6, 6.4.6.1. > > [R] selected from submenu OF allows you to save the graphics screen output of the CLUSTER session as a raw binary file defining the pixel image. Pixel images are identical to those displayed in graphics mode except that character output (used for titles, lables, and menus in the graphics window) is suppressed. Raw binary format files can be used outside BALSAC to produce image sequences for animation or fast display of fixed views, see Sec. 6.4.7. The prompt Image size (Lwx,Lwy): asks for the actual size of the pixel image to be saved. This is given by two lengths, Lpx (horizontal) and Lpy (vertical), defined in pixel units. The numbers Lwx, Lwy shown in the prompt refer to the pixel size of the present graphics window. If BALSAC is run in batch mode the above prompt does not show and the saved image agrees in pixel size with that of the graphics window. NOTE that this option is available only with the Unix/X.11 version of BALSAC. > > [I] selected from submenu OF switches the initialization option flag fin between "on" and "off" where the present setting is shown in the prompt "[I]nit(fin)" of submenu OF. For fin = "on" all PLOT3D or LATUSE format file output includes additional initialization information with parameters identical to those of the initialization file, see Sec. 6.4.10. This allows you to save all present color assignments and adapter/window parameters together with the structural data of the lattice section. Clusters where atom colors have been changed inside a BALSAC/CLUSTER session, see Sec. 6.3.12.2, MUST be saved with fin = "on". Otherwise, all color assignments will be lost and replaced by defaults taken from the (default) initialization file. > > [O] selected from submenu OF switches the logo option flag flg between "on" and "off" where the present setting is shown in the prompt "l[O]go(flg)" of submenu OF. For flg = "on" all PostScript file output includes an additional logo "BALSAC plot" to be shown at the bottom right of the print. This allows you to indicate the origin of BALSAC graphics output which is a matter of curtesy to the author and may be needed to comply with legal requirements. > > [,] selected from submenu OF closes the open output file and returns to the BALSAC/CLUSTER main option menu. > [Q] selected from submenu O opens the quicksave file 'balsac.plt' in your working directory and all structure and graphics data of the present BALSAC/CLUSTER session are saved on this file (using PLOT3D format). After this file 'balsac.plt' is closed and BALSAC returns to its CLUSTER main option menu. The quicksave option offers a fast method to store structure data on a file for later retrieval. Quicksave files may be used for structure input to subsequent BALSAC/CLUSTER sessions. > [I] selected from submenu O switches the initialization option flag fin between "on" and "off" where the present setting is shown in the prompt "[I]nit(fin)" of submenu O. This option is identical to option [I] of the file format menu OF discussed above. > [O] selected from submenu O switches the logo option flag flg between "on" and "off" where the present setting is shown in the prompt "l[O]go(flg)" of submenu O. This option is identical to option [O] of the file format menu OF discussed above. > [,] selected from submenu O returns immediately to the BALSAC/CLUSTER main option menu without file output. next, previous Section / Table of Contents / Index