6.4.3. PLOT3D FORMAT (IN/OUTPUT FROM CLUSTER/LATTICE SESSION)

next, previous Section / Table of Contents / Index This is the second of two file formats accepted for input by BALSAC and is used for structure/graphics/option parameter definitions in BALSAC/CLUSTER sessions. The format is only slightly different (Cards 1, 1a) from and compatible with the standard PLOT3D format ((C) Copyright 1992 K. Hermann, version 3.0 or later) as proposed in the SARCH/LATUSE/PLOT3D ((C) Copyright 1992 M. A. Van Hove and K. Hermann) software package. Therefore, structure files generated with PLOT3D can be used for input to BALSAC/CLUSTER and vice versa. The PLOT3D type structure file format is defined by 5 Cards given as follows: Card 1. (A60,I5) TITLE,NBATCH TITLE := Title of the cluster. NBATCH := Number of options requested for a CLUSTER batch run (default = 0). The internal maximum is 48. Card 1a. (48A1) (BOPT(I),I=1,NBATCH) This Card is needed ONLY if NBATCH > 0. BOPT(I) := Array of batch option flags (one character each). These flags determine the run sequence of a CLUSTER session in batch mode. Some options require additional input given on Cards at the end of the file. The following table lists all available options with their character codes BOBT, see Sec. 6.3.0, and indicates additional card input at the file end. The flag codes MUST be given by upper case characters. ------------------------------------------------------- main option BOPT add. Cards # ------------------------------------------------------- Finish BALSAC/CLUSTER run , -- Structure option S 1 - 5f Radii / nuclear charge option R -- View option V 4, 4a Graphics option G 5, 5a(-f) Output on structure file O see below Execute (plot/list) X -- New structure from scratch N -- Input of structure file I Sec. 6.3.9 Transfer to LATTICE (exit) L -- Analyze cluster A -- Basic parameter option P -- Refresh menu /interactive mode E -- File stack option K -- Redefine cluster title T -- ------------------------------------------------------- After all option flags are used in batch mode BALSAC returns to interactive mode showing the CLUSTER main option menu unless the last flag reads "," (exit) or "L" (transfer) after which BALSAC finishes. If a batch run requests file output then additional Cards 1' (I2,A72) NFRM,FIL2O have to be added at the end of the file with NFRM := Parameter defining the output file format. ---------------------------------------- NFRM format ---------------------------------------- 0 standard LATUSE 3 gray scale PostScript 4 PLOT3D 5 SCHAKAL 6 color PostScript 9 XYZ (Xmol) 12 Raw binary (pixel image) ---------------------------------------- FILE2O := Name of output file used in batch mode. The file name is restricted to 72 characters. Card 2. (I5,3F15.9) NKTOT,XTOT,YTOT,ZTOT NKTOT := Number of atoms listed by coordinates below. XTOT,YTOT,ZTOT := Size of block (lengths along x, y, z) containing all atoms. Card(s) 3. (4F15.9,I4) X(I),Y(I),Z(I),RAD(I),NUC(I),I=1,NKTOT X(I),Y(I),Z(I) := Cartesian coordinates of the Ith atom in the cluster. RAD(I) := Sphere radius assigned to the Ith atom. NUC(I) := Nuclear (element) charge assigned to the Ith atom. Card 4. (5F12.5,12X,I5) THETA,PHI,ROT,MAGNF,PERSP,NFOC THETA,PHI := Polar and azimuthal angles of the viewing direction with respect to the coordinate system of the cluster used in the graphical output. ROT := Rotation angle about the viewing direction used in the graphical output. MAGNF := Magnification factor used in the graphical output. PERSP := Perspective distance factor used in the graphical output. PERSP = 0 or PERSP >> 1 refer to parallel projection while PERSP > 0 means central projection. NFOC := Viewing focus definition. NFOC = 0 : The viewing focus coincides with the center of the lattice section, see Sec. 5.1. NFOC > 0 : After the cluster is built the center of atom number NFOC will serve as center to set the viewing focus. Here Card 4a has to be included but its coordinates are used only if NFOC exceeds the maximum number of atoms in the section. NFOC = -1 : The viewing focus is given explicitly by cartesian coordinates on Card 4a. Card 4a. (3F12.5) ORX,ORY,ORZ This Card is needed ONLY if NFOC > 0 or NFOC < 0. ORX,ORY,ORZ := Cartesian coordinates of the viewing focus used for graphics output. The focus will project on to the center of the screen if no additional shifting is applied, cp. Card 5. This Card is identical with Card 10a of the LATUSE file format, see Sec. 6.4.2. Card 5. (8I5) M,N,ICLC,IBFT,NSHX,NSHY,ICON,INITSV M := Compound index to define display and graphics mode, see Sec. 6.3.5. Here M = SF * (10 * K + L) where SF = 1 for mono viewing, = -1 for stereo duplication. K = 0, 1 for atom-by-atom display mode, L = 0 for no plot/listing output (testing purposes), = 1 for atom coordinate listing, no graphics, = 2 for atoms plotted as color dots (small circles), = 3 for atoms plotted as color circles, = 4 for atoms plotted as color filled circles, = 5 for atoms plotted as red/blue stereo circles, = 6 for atoms plotted as hard-shaded balls, = 7 for atoms plotted as fuzzy-shaded balls, = 8 for atoms plotted as dither-shaded balls, = 9 for atoms plotted as glossy-shaded balls. N := Compound index to define color codes for atom painting and background used in graphical output, see Sec. 6.3.5. Here N = 100 * B + C where B denotes the background color and C denotes the starting value of the color palette used to paint atoms. ICLC := Compound flag for discriminating atoms by colors and for labeling atoms. The definition is given in the following table -------------------------------------- ICLC color discr. label -------------------------------------- 1 elements none 2 elements element symbol 3 elements number -------------------------------------- IBFT := Compound flag for displaying a title line, drawing a wire frame about the lattice section. The definition is given in the following table ----------------------- IBFT title frame ----------------------- 0 no no 1 no yes 4 yes no 5 yes yes ----------------------- NSHX,NSHY := Horizontal and vertical shift of the plot origin in pixel units, see Sec. 6.3.5. ICON := Total number of link constraints used to connect atoms by straight lines or sticks in the plot. ICON = 0 will not connect while ICON > 0 requires ICON additional Cards 5a to define the constraints. INITSV := Flag for including initialization information in the LATUSE and PLOT3D format output files. = 0 no initialization information is included. = 1 initialization information is included in the output file. The parameters are contained on Cards 5b-f which are identical to Cards 1 - 5 of the initialization file, see Sec. 6.4.10. Here ICON > 0 Cards 5a follow. Card(s) 5a. (2I5,3D15.7,I5) NUCA(I),NUCE(I),RMIN(I),RMAX(I), RBOND(I),NBCOL(I),I=1,ICON These cards appear only if ICON > 0. NUCA(I),NUCE(I) := NUCA > NUCE > 0 connects atoms of charge NUCA with those of charge NUCE within the defined distance range, NUCA > NUCE = 0 connects atoms of charge NUCA with all others within the defined distance range, NUCA = NUCE = 0 connects every two atoms within the defined distance range. NUCA < 0, NUCE < 0 connects atoms number -NUCA and -NUCE independent of the distance. RMIN(I),RMAX(I) := Minimum and maximum distances used for connecting atoms by lines / sticks (Ith connection constraint). These values have no meaning and are set to zero if NUCA < 0, NUCE < 0. RBOND(I) := Radius of the cylindrical sticks connecting between atoms. If RBOND = 0 atoms are connected by straight lines. NBCOL(I) := Color code (absolute value) used to paint connecting lines / sticks. Cards 5b-f. are needed only for INITSV = 1, see Card 5. They are identical in format to Cards 1 - 5 of the initialization file, see Sec. 6.4.10. Cards 5,5a-f are identical with Cards 11,11a-f of the LATUSE file format, see Sec. 6.4.2. The following listing shows as an example the output file of an interactive BALSAC/CLUSTER session with input similar to the one discussed in the tutorial. Here the initialization parameters (Cards 5b-f.) are included in the file. The sequence of lines refers to Cards no. 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5a, 5a, 5b, 5c, 5d, 5e, 5e, 5f, 5f, 5f, 5f. ----------------------------------------------------------------------------- Ni(CO)4 molecule 0 9 9.906002283 9.906002283 9.906002283 0.000000000 0.000000000 0.000000000 1.547001240 28 -2.164999960 -2.164999960 -2.164999960 1.016538620 6 -3.405999900 -3.405999900 -3.405999900 1.132936360 8 2.164999960 2.164999960 -2.164999960 1.016538620 6 3.405999900 3.405999900 -3.405999900 1.132936360 8 3.405999900 -3.405999900 3.405999900 1.132936360 8 2.164999960 -2.164999960 2.164999960 1.016538620 6 -2.164999960 2.164999960 2.164999960 1.016538620 6 -3.405999900 3.405999900 3.405999900 1.132936360 8 80.00000 -10.00000 0.00000 1.00000 3.00000 0 6 1 1 5 0 0 2 1 6 0 0.3700000D+01 0.3800000D+01 0.2000000D+00 8 8 6 0.2100000D+01 0.2200000D+01 0.1000000D+00 12 0 0 640 480 1.0000 63 4 3 18 16 8 16 .2000 .4000 .4000 65.0000 -25.0000 .3000 -320.0000 4 1 2 3 4 0 0 0 63 63 63 0 0 0 63 63 63 63 63 63 63 0 0 0 0 63 63 63 638x13bold 0 0 50 .3000 .4000 .7000 .8000 1.0000 0 63 0 .2000 .3000 .7000 .8000 1.0000 0 63 50 .3000 .4000 .7000 .8000 1.0000 63 0 0 .2000 .3000 .7000 .8000 1.0000 ----------------------------------------------------------------------------- next, previous Section / Table of Contents / Index