6.4.2. LATUSE FORMAT (IN/OUTPUT FROM LATTICE/CLUSTER SESSION)

next, previous Section / Table of Contents / Index This is the first of two file formats accepted for input by BALSAC and is used for structure/graphics/option parameter definitions in BALSAC/LATTICE sessions. The format is identical to the standard LATUSE 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 LATUSE can be used for input to BALSAC/LATTICE and vice versa. The LATUSE type structure file format is defined by 20 Cards given as follows: Card 1. (I6,I2,A20,I2,48A1) NDLAY,NFRM,FIL2O,NBATCH,(BOPT(I),I=1,NBATCH) or (I6,I2,A20,I2,24I2) NDLAY,NFRM,FIL2O,NBATCH,(IOPT(I),I=1,NBATCH) NDLAY := Delay parameter used in batch mode for waiting between subsequent layers in layer-by-layer plots. On an 100 MHz Pentium PC NDELAY = 100000 corresponds to a delay time of about 1.5 sec. NFRM := Parameter defining the output file format (FILE2O) used in LATTICE batch runs, see below. ------------------------------------------------ NFRM format ------------------------------------------------ 0 standard LATUSE 1 extended LATUSE 2 SARCH ASCII 3 gray scale PostScript 4 PLOT3D 5 SCHAKAL 6 color PostScript 7 Wigner-Seitz cell (PostScript, frame) 8 Brillouin zone (PostScript, frame) 9 XYZ (Xmol) 12 Raw binary (pixel image) ------------------------------------------------ FILE2O := Name of output file used for first file output in batch mode. Note that this file name is restricted to 20 characters. If a batch run requests more than one file output then additional Cards 1' (I2,A72) NFRM,FIL2O have to be added at the end of the file. Here file names are restricted to 72 characters. NBATCH := Number of options requested for a LATTICE batch run (default = 1). The internal maximum is 48 (24 for old input format). BOPT(I) := Array of batch option flags (one character each). These flags determine the run sequence of a LATTICE 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. 6.2.0, and indicates additional card input at the file end. The flag codes MUST be given by upper case characters. ----------------------------------------------------------- main option BOPT IOPT add. Cards # ----------------------------------------------------------- Finish BALSAC/LATTICE run , 0 -- Lattice definition L 1 2 - 5a Radii / nuclear charge option R 2 -- Miller index definition M 3 6 Section definition S 4 7 Change layer structure C 5 8 - 9b View option V 6 10, 10a Graphics option G 7 11, 11a(-f) Output on structure file O 8 see Card 1 Execute (plot/list) X 9 -- New structure from scratch N 10 -- Input of structure file I 11 Sec. 6.2.11 Refresh menu /interactive mode E 12 -- Transfer to CLUSTER (exit) U 13 -- Analyze lattice section A 14 -- Basic parameter option P 15 -- File stack option K 16 -- Define atoms without plotting Y 17 -- ----------------------------------------------------------- After all option flags are used in batch mode BALSAC returns to interactive mode showing the LATTICE main option menu unless the last flag reads "," (exit) or "U" (transfer) after which BALSAC finishes. NOTE that in the old LATUSE format option flags are given by integers IOPT rather than characters BOPT. The values of IOPT corresponding to each option are included in the table above. BALSAC accepts both flag formats (no mixture of the two!). Card 2. (I5,F15.9,A40) NTYPV,ACON,GITNA NTYPV := Lattice type parameter. The following table shows all possible values ------------------------------------------------------------- NTYPV lattice type ------------------------------------------------------------- 1 simple cubic 2 (-2) fcc , cubic (Bravais) Miller indices 3 (-3) bcc , cubic (Bravais) Miller indices 4 (-4) hcp , Bravais (4-index) Miller indices 5 (-5) diamond , cubic (Bravais) Miller indices 6 (-6) NaCl , cubic (Bravais) Miller indices 7 CsCl , cubic Miller indices 8 (-8) Zincblende , cubic (Bravais) Miller indices 9 (-9) Graphite , Bravais (4-index) Miller indices 10 (-10) free Lattice , Bravais (4-index) Miller indices 10 all 14 Bravais lattices implemented in BALSAC ------------------------------------------------------------- ACON := Global lattice constant. All structural parameters (lattice vectors, lattice basis vectors, radii; Cards 3,4,5) will be renormalized inside BALSAC by multiplying with the value of ACON. GITNA := Lattice type name, see Sec. 6.2.1. Cards 3. (3(3F15.9/)) ((R(I,J),I=1,3),J=1,3) R(I,J) := Lattice vectors (Ith component if Jth vector in cartesian coordinates). These data are ignored for standard lattices defined by code numbers NTYPV = 1 - 9 where the lattice geometry is provided internally but an appropriate number of (dummy) Cards has to be given, see Sec. 6.2.1. Card 4. (2I5) NBG,NSYEL NBG := Values |NBG| define the number of lattice basis vectors. Both positive and negative NBG values are possible, see Cards 5. For primitive lattices set NBG = 1, see Sec. 6.2.1. NSYEL := Number of point symmetry elements of the bulk lattice, see Secs. 5.3, 6.2.14.1. NOTE that this parameter is obsolete since the full lattice symmetry is now computed internally. NSYM is included only to comply with in/output of previous BALSAC (LATUSE) versions. For NSYEL > 0 additional input on Cards 5a must be provided (see below). Card(s) 5. (4F15.9,I10) ((RBG(I,J),I=1,3),RKG(J),NUC(J),J=1,|NBG|) RBG(I,J) := Definition of lattice basis vectors. NBG > 0 : lattice basis vectors are given in absolute cartesian coordinates where RBG(I,J) denotes the Ith component of Jth lattice basis vector, J=1,NBG. For primitive lattices set RBG(I,1) = 0.0. NBG < 0 : lattice basis vectors are given by linear combinations of lattice vectors where RBG(I,J) denotes the weight of the Ith lattice vector contributing to the Jth lattice basis vector, J =1,NBG. RKG(J) := Atom radii defined for atoms assigned to the Jth lattice basis vector. If any of the RKG(J) = 0 all RKG values are ignored and (rescaled) default atomic radii are used such that maximum space filling is achieved (touching spheres geometry). Radii may be changed interactively, see Secs. 6.2.1-2. NUC(J) := Nuclear (element) charge of atoms assigned to the Jth lattice basis vector. These values may be changed interactively, see Secs. 6.2.1-2. Card(s) 5a. (3F15.9,A4) ((VSYEL(I,J),I=1,3),SYEL(J),J=1,NSYEL) These Cards are needed ONLY if NSYEL > 0. NOTE that these cards are obsolete and their content is ignored since the full lattice symmetry is now computed internally. They are included only to comply with in/output of previous BALSAC (LATUSE) versions. VSYEL(I,J) := Ith component (I=1,3) of Jth point symmetry element vector. These vectors are defined according to the symmetry elements given by SYEL(J), see below and Secs. 5.3, 6.2.14.1. SYEL(J) := Definition label of the Jth point symmetry element. Label "Cn " defines an n-fold rotational axis (n=1,2,3,4,6) with VSYEL(I,J), I=1,3 being the axis direction, "M " defines a mirror plane with VSYEL(I,J), I=1,3 being the mirror plane normal. Card 6. (4I5) I1,I2,I3,I4S I1,I2,I3 := Miller indices of lattice net planes to be used for stacking to form the lattice block. I4S := In 4-index notation of hexagonal lattices (lattice options = -4,-9,-10) a meaningful I4S value has to be given, see Sec. 6.2.3. In the conventional 3-index notation I4S is ignored (set to 0) by default. Card 7. (4I5,5F10.3) NZ1,NZ2,NZ3,NINIT, XSPH,YSPH,ZSPH,RMIN,RMAX NZ1,NZ2 := Number of atoms along R1, R2 included in the basic lattice section (block of rectangular base area) used for graphical (numerical) output. NZ3 := Number of net planes included in the basic lattice section used for graphical (numerical) output. NINIT := Index number of the starting plane (termination plane, meaningful for non- primitive lattices, otherwise ignored). XSPH,YSPH,ZSPH := Cartesian coordinates of the center of a spherical shell used as an additional boundary, see Sec. 6.2.4. RMIN,RMAX := Inner/outer radii of a spherical shell used as an additional boundary, see Sec. 6.2.4. Card 8. (12I5) NRCLX,(IRR(I),I=1,NRCLX) NRCLX := Number of planes to be restructured (NRCLX < 11). For NRCLX = 0 no restructuring is assumed. IRR(I) := Layer index of Ith plane to be restructured. Valid numbers are between 1 and NZ3. NRCLX sets of Cards 9a, 9b follow. Card(s) 9a. (I5,7F10.6) (NBSR(I),XSR1(I),XSR2(I),XSR3(I), RM11(I),RM12(I),RM21(I),RM22(I),I=1,NRCLX) These Cards are needed ONLY if NRCLX > 0. NBSR(I) := Restructure index of the Ith layer. For values NBSR(I) = 0 layer restructuring uses the unmodified planar lattice basis of the Ith layer, > 0 layer restructuring starts from a separate lattice basis set for the Ith layer with NBSR(I) inequivalent atoms to be described on Card(s) 9b. XSRj(I) := Components (j=1,2,3) of the layer shift vector used to shift the Ith layer rigidly (allowing for layer relaxation, see Sec. 6.2.5.) RMjk(I) := Components (j,k=1,2) of the 2x2 transformation matrix defining the modified periodicity vectors of the Ith restructured layer in terms of the unstructured layer basis, see Sec. 6.2.5. Here NBSR(I) Cards 9b follow. Card(s) 9b. (4F10.6,I5) (RBGR(J,K,I),J=1,3),RKGR(K,I),NUCR(K,I), K=1,NBSR(I)) These Cards are needed ONLY if NBSR(I) > 0. RBGR(J,K,I) := Components (J=1,2,3) of the Kth separate lattice basis vector assigned to the Ith plane to be restructured. The vectors are described as linear combinations of the two (modified) layer periodicity vectors (components J=1,2, see Card 9a) plus a coordinate perpendicular to the layer (component J=3) given in multiples of the distance between equivalent layers of the unperturbed lattice structure. RKGR(K,I) := Atom radius defined for atoms assigned to the Kth lattice basis vector of the Ith restructured layer. These values may be changed interactively, see Secs. 6.2.2, 6.2.5. NUCR(K,I) := Nuclear (element) charge associated with atoms located at the Kth lattice basis vector of the Ith restructured layer. These values may be changed interactively, see Secs. 6.2.2, 6.2.5. Card 10. (5F12.5,12X,I5) THETA,PHI,ROT,MAGNF,PERSP,NFOC THETA,PHI := Polar and azimuthal angles of the viewing direction with respect to the lattice plane normal vector 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 lattice section is built the center of atom number NFOC will serve as center to set the viewing focus. Note that atom numbers depend on the section shape and size. Here Card 10a 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 10a. Card 10a. (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 11. Card 11. (8I5) M,N,ICLC,IBFT,NSHX,NSHY,ICON,INITSV M := Compound index to define display and graphics mode, see Sec. 6.2.7. Here M = SF * (10 * K + L) where SF = 1 for mono viewing, = -1 for stereo duplication. K = 0 for layer-by-layer display mode, = 1 for atom-by-atom display mode, = 2 for cell-by-cell-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. 6.2.7. 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 4 layers none 5 layers element symbol 6 layers number -------------------------------------- IBFT := Compound flag for displaying a title line, sketching lattice vectors, drawing a wire frame about the lattice section. The definition is given in the following table ------------------------------- IBFT title basis frame ------------------------------- 0 no no no 1 no no yes 2 no yes no 3 no yes yes 4 yes no no 5 yes no yes 6 yes yes no 7 yes yes yes ------------------------------- NSHX,NSHY := Horizontal and vertical shift of the plot origin in pixel units, see Sec. 6.2.7. 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 11a 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 11b-f which are identical to Cards 1 - 5 of the initialization file, see Sec. 6.4.10. Here ICON > 0 Cards 11a follow. Card(s) 11a. (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 11b-f. are needed only for INITSV = 1, see Card 11. They are identical in format to Cards 1 - 5 of the initialization file, see Sec. 6.4.10. Cards 1. - 11f. form the complete input file to a LATTICE session. Batch options on the input file may require additional input added after this standard input set, see Sec. 3.4. If the LATUSE format file has been generated in a BALSAC/LATTICE session it will contain additional output (Cards 12-20) described in the following. Card 12. (7I5) I1,I2,I3,I1S,I2S,I3S,I4S I1,I2,I3 := Miller indices of the lattice planes in terms of the Bravais reciprocal lattice vectors. I1S,I2S,I3S := Miller indices in simple cubic notation for sc-, fcc-, bcc-derived lattices (options = 2,3,5,6,8). I4S := 4th component of Miller indices in 4-index notation for hexagonal lattices (options =-4,-9,-10). For other lattices IS4=0. Cards 13. (4F15.9,3(/3I5,3F15.9)) (GM(I),I=1,3),DN,((NN(I,J),I=1,3),(GZ(I,J),I=1,3),J=1,3) GM(I) := Ith cartesian component of the lattice net plane normal vector. DN := Distance between subsequent equivalent net planes. NN(I,J) := Ith component of the Jth lattice vector defining lattice net planes (NN(I,1) and NN(I,2) refer to vectors in the planes and NN(I,3) point between adjacent planes). This definition is with respect to the original lattice vectors of the direct lattice. GZ(I,J) := Ith component of the Jth lattice vector defining lattice net planes ( GZ(I,1) and GZ(I,2) refer to vectors in the planes and GZ(I,3) point between adjacent planes). This definition is given in absolute cartesian coordinates. Card 14. (9I5) ((NNT(J,I),J=1,3),I=1,3) NNT(J,I) := Components of the original lattice vectors given in the basis of the transformed lattice vectors. The Ith original lattice vector is defined by components (NNT(I,1), NNT(I,2), NNT(I,3)). Card 15. (2I5) NEQ,NSYSUR NEQ := Number of non-equivalent net planes (subplanes) between subsequent main lattice net planes in the case of non-primitive lattices. For primitive lattices NEQ = 1. NSYSUR := Number of point bulk symmetry elements that survive in the (surface) lattice planes defined by I1, I2, I3. Card(s) 16. (3(A5,F15.9)) (LAYP(I),DD(I),I=1,NEQ) LAYP(I) := ASCII label of the Ith non-equivalent subplane (A, B, C,...). DD(I) := Distance of the Ith non-equivalent subplane from the main lattice plane. Card 17. (4F15.9,I5,A5) ((PP(I,J),I=1,3),RKG(J),NUC(J),LAY(J),J=1,NBG) PP(I,J) := Ith component of the Jth lattice basis vector in non- primitive lattices defined with respect to the transformed lattice periodicity vectors GZ(I,J) (see Cards 13). RKG(J) := Atom radius of atoms assigned to the Jth lattice basis vector. NUC(J) := Nuclear charge of atoms assigned to the Jth lattice basis vector (see Card 5). LAY(J) := ASCII label of the Jth lattice basis vector denoting the non-equivalent subplane in non-primitive lattices (see Card 15). Card(s) 18. (3F15.9,A4) ((VSYELS(I,J),I=1,3),SYEL(J),J=1,NSYSUR) These Cards appear ONLY if NSYSUR > 0. VSYELS(I,J) := Ith component of Jth surviving point symmetry element vector. Vectors are defined according to the symmetry elements given by SYEL(J). SYEL(J) := Definition label of the Jth point symmetry element. Here a label "1 " defines the identity operation, "I " defines the inversion operation, 'Cn' defines an n-fold rotational axis (n=2,3,4,6) with VSYEL(I,J), I=1,3 along the axis, 'Mn' defines an n-fold mirror plane (n=2,3,4,6) with VSYEL(I,J), I=1,3 along the mirror plane normal. Note that M2 denotes standard mirror planes while Mn, n = 3, 4, 6 refer to n-fold rotations combined with inversions. The symmetry labels SYEL(J) are restricted to 4 characters where leading blanks can appear before the first character ('C' or 'M'). Card 19. (I5,3F15.9) NKTOT,XTOT,YTOT,ZTOT This Card appears only if NFRM = 1 (Card 1) or if extended LATUSE output format was chosen in the LATTICE session. NKTOT := Number of atoms included in the section. XTOT,YTOT,ZTOT := Size of block (lengths along x, y, z) containing all atoms of the section. Card(s) 20. (4F15.9,I4) (XSRT(I),YSRT(I),ZSRT(I),RSRT(I),NCSRT(I), I=1,NKTOT) This Card appears only if NFRM = 1 (Card 1) or if extended LATUSE output format was chosen in the LATTICE session with NKTOT > 0. XSRT(I),YSRT(I),ZSRT(I) := Cartesian coordinates of the Ith atom included in the section. RSRT(I) := Sphere radius of the Ith atom included in the section. NCSRT(I) := Nuclear (element) charge of the Ith atom included in the section. The following listing shows as an example the output file of an interactive BALSAC/LATTICE session with input similar to the one discussed in the tutorial. The sequence of lines refers to Cards no. 1, 2, 3, 3, 3, 4, 5, 5, 6, 7, 8, 9a, 9b, 10, 11, 11a,12, 13, 13, 13, 13, 14, 15, 16, 17, 17, 18, 18, 18, 19, 20, ..., 20. ----------------------------------------------------------------------------- 50 1 1E 8 1.000000000 Znblnde(fcc+2) lattice 0.000000000 0.500000000 0.500000000 0.500000000 0.000000000 0.500000000 0.500000000 0.500000000 0.000000000 2 0 0.000000000 0.000000000 0.000000000 0.139643663 30 0.250000000 0.250000000 0.250000000 0.293369039 16 0 0 1 0 3 4 7 1 0.000 0.000 0.000 0.000 0.000 1 4 1 0.000000 0.000000 0.000000 0.500000 1.000000 -0.500000 1.000000 0.000000 0.000000 0.000000 0.100000 8 0.00000 0.00000 0.00000 1.00000 0.00000 0 16 1 1 7 0 0 1 0 8 8 0.7000000D+00 0.8000000D+00 0.0000000D+00 7 1 1 0 0 0 1 0 0.000000000 0.000000000 1.000000000 0.500000000 0 0 1 0.500000000 0.500000000 0.000000000 1 -1 0 -0.500000000 0.500000000 0.000000000 1 0 0 0.000000000 0.500000000 0.500000000 0 0 1 0 -1 1 1 0 0 2 8 A 0.000000000 B 0.250000000 0.000000000 0.000000000 0.000000000 0.139643663 30 A 0.250000000 0.750000000 0.500000000 0.293369039 16 B 0.000000000 0.000000000 0.000000000 1 0.000000000 0.000000000 1.000000000 C2 0.000000000 0.000000000 1.000000000 C4 0.000000000 0.000000000 0.000000000 I 0.707106781 -0.707106781 0.000000000 M2 1.000000000 0.000000000 0.000000000 M2 0.000000000 1.000000000 0.000000000 M2 0.707106781 0.707106781 0.000000000 M2 59 2.000951640 2.708058422 2.086738078 0.000000000 0.000000000 0.000000000 0.139643669 30 ... 1.060660172 1.767766953 1.500000000 .139643663 30 ----------------------------------------------------------------------------- next, previous Section / Table of Contents / Index