6.2.8. 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/LATTICE session on output files. These files can be used as input to subsequent BALSAC/LATTICE 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 as well as a binary pixel image format. Since all structure output files (except for pixel images) are fixed format ASCII-type they can be easily modified with a text editor outside BALSAC. The file output menu O reads ============= FILE STORE OPTIONS ===================================== Latest input = {inputfilename} [F]ilesave [Q]uicksave [B]asis(bvr) [I]nit(fin) l[O]go(flg) [?,]esc ================================================================ 44 == where the present settings of the basis vector representation bvr (reading "abs" or "rel", see below) as well as 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: [L]at [E]xtlat [P]lt [S]ar sch[K]l [D]pdb [F]xyz [G]ps [C]olps [W]sc [B]z {[R]bin} [I]nit(fin) l[O]go(flg) [?,]esc ================================================================ 45 == allows you to select the format of the output file (and change the initialization and logo option flags). > > [L] selected from submenu OF saves all structure and graphics data of the present BALSAC/LATTICE 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 LATTICE main option menu. For non-primitive lattices the lattice basis vectors can be stored in absolute coordinates or in relative units (multiples of lattice vectors) depending on the present setting shown as bvr ("abs" or "rel") in menu O. The setting can be changed with option [B] of menu O, see below. 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. The output file includes by default one batch option flag,"E", (see Card 1 of the LATUSE format) such that BALSAC/LATTICE batch runs using this file for input will only construct the lattice section and move to the main option menu, see also Sec. 3.4. > > [E] selected from submenu OF saves all structure and graphics data of the present BALSAC/LATTICE session using extended LATUSE format (Cards 1-20), see Sec. 6.4.2. This is confirmed by Saving data on file : Extended LATUSE format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its LATTICE main option menu. The extended LATUSE format differs from the standard LATUSE format only by the additional Cards 19, 20 which list coordinates, radii and nuclear charges of all atoms of the lattice section. > > [P] selected from submenu OF saves all structure and graphics data of the present BALSAC/LATTICE 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 LATTICE main option menu. Here the present lattice section will be interpreted as a fictitious cluster saving all its atom coordinates, radii, and nuclear charges but no information concerning the lattice periodicity will be saved in the file. 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. > > [S] selected from submenu OF saves all structure data of the present BALSAC/LATTICE session using SARCH ASCII format, see Sec. 6.4.4. This is confirmed by Saving data on file : SARCH ASCII format File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its LATTICE main option menu. Output files of SARCH ASCII format can be used as input to SARCH ((C) Copyright 1991-5 M. A. Van Hove), a PC based analysis and visualization program including LEED and STM simulation, see Sec. 1.3. BALSAC uses only a restricted SARCH ASCII format as described in Sec. 6.4.4. This format cannot account for all structural features available with SARCH. For further details consult the SARCH documentation. > > [K] selected from submenu OF saves all structure data of the present BALSAC/LATTICE 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 LATTICE 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/LATTICE 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 LATTICE 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/LATTICE 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 LATTICE 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/LATTICE session using (encapsulated) gray scale ([G]) or color ([C]) PostScript format, see Sec. 6.4.6. If fuzzy-, dithered-, 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 LATTICE 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. > > [W] selected from submenu OF allows you to create a gray scale PostScript plot file displaying the present 3-dimensional Wigner-Seitz elementary cell. The shape and orientation of the cell is determined by the actual viewing parameters theta, phi, rot, magnf, and persp, see Sec. 6.2.6, and is analogous to the Wigner-Seitz cell screen output with the graphic analysis, see Sec. 6.2.14.2. The prompt =================================================================== Wigner-Seitz cell layout: [F]rame [S]hade [B]oth [N]N+both [?,]esc ============================================================= 78 == asks for different layouts of the Wigner-Seitz cell plot where selecting [F] draws the cell as a transparent wire frame. [S] draws the cell as a shaded opaque polyhedron where only front polygon sections are visible. [B] draws the cell as a shaded transparent polyhedron where the edges are emphasized visually by black lines. [N] draws the cell as a shaded transparent polyhedron where the edges are emphasized visually by black lines and additional sticks point to nearest neighbor atoms. [,] returns immediately to the BALSAC/LATTICE main option menu without a file saved. The output is confirmed by Saving data on file : Wigner-Seitz cell (PostScript) File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its LATTICE main option menu. > > [B] selected from submenu OF allows you to create a gray scale PostScript plot file displaying the present 3-dimensional Brillouin zone (Wigner-Seitz of the reciprocal lattice). The orientation of the cell is determined by the actual viewing parameters theta, phi, rot, magnf, and persp, see Sec. 6.2.6, and is analogous to the Brillouin zone screen output with the graphic analysis, see Sec. 6.2.14.2. The prompt =================================================================== Brillouin zone layout: [F]rame [S]hade [B]oth [N]N+both [?,]esc ============================================================= 78 == asks for different layouts of the Brillouin zone plot where selecting [F] draws the zone as a transparent wire frame. [S] draws the zone as a shaded opaque polyhedron where only front polygon sections are visible. [B] draws the zone as a shaded transparent polyhedron where the edges are emphasized visually by black lines. [N] draws the zone as a shaded transparent polyhedron where the edges are emphasized visually by black lines and additional sticks point to nearest neighbor atoms of the reciprocal lattice. [,] returns immediately to the BALSAC/LATTICE main option menu without a file saved. The output is confirmed by Saving data on file : Brillouin zone (PostScript) File output completed ** Press [C], L-click to continue ** (DOS only) after which the file is closed and BALSAC returns to its LATTICE main option menu. > > [R] selected from submenu OF allows you to save the graphics screen output of the LATTICE 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 (extended) 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. Lattice sections where atom colors have been changed inside a BALSAC/LATTICE session, see Sec. 6.2.14.2, 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/LATTICE main option menu. > [Q] selected from submenu O opens the quicksave file 'balsac.lat' in your working directory and all structure and graphics data of the present BALSAC/LATTICE session are saved on this file (using standard LATUSE format). After this file 'balsac.lat' is closed and BALSAC returns to its LATTICE 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/LATTICE sessions. > [B] selected from submenu O switches between two representations of lattice basis vectors for non-primitive lattices used in LATUSE format file output. The lattice basis vectors can be defined by absolute coordinates or by relative units (multiples of lattice vectors). The present setting is shown as parameter bvr ("abs" for absolute coordinates, "rel" for relative units) in menu O. > [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/LATTICE main option menu without file output. Note that file output in any format which includes atom coordinates requires BALSAC to have plotted/listed the lattice section at least once (using the execute option [X] which among other things calculates coordinates). Otherwise a warning NO file output : atoms undefined or incomplete is displayed and no output file is generated. Note further that in BALSAC/LATTICE sessions the complete set of atoms of a lattice section can be saved on files ONLY if atom-by-atom or cell-by-cell display mode was chosen, see Sec. 6.2.7. For layer-by-layer mode any file store (except standard LATUSE format) shows a warning prompt WARNING! layer-by-layer mode, atoms incomplete (?) : [S]tore [?,]esc Selecting [S] in this prompt saves only coordinates of the atoms included in the section layer displayed last which is confirmed by File output completed ** Press [C], L-click to continue ** (DOS only) while selecting [,] will not save atoms on file as indicated by NO file output : atoms undefined or incomplete If BALSAC/LATTICE is run in batch mode the format of possible file output is determined by parameter NFRM in the input file (Card 1 of the LATUSE format, see Sec. 6.4.2). The following table lists NFRM values for all output formats available in batch runs together with respective option keys of submenu OF. ---------------------------------------------------- format key NFRM ---------------------------------------------------- standard LATUSE [L] 0 extended LATUSE [E] 1 SARCH ASCII [S] 2 Gray scale PostScript [G] 3 PLOT3D [P] 4 SCHAKAL [K] 5 Color PostScript [C] 6 Wigner-Seitz cell (PostScript, frame) [W] 7 Brillouin zone (PostScript, frame) [B] 8 XYZ (Xmol) [F] 9 Raw binary (pixel image) [R] 12 ---------------------------------------------------- next, previous Section / Table of Contents / Index