============================================================================== K R I B E R : U S E R M A N U A L Version 1.0 (January 1991) ============================================================================== 2. General remarks =============== 2.1 Atom positions -------------- For each atom, a label, the fractional coordinates and the coordination number have to be given. The label is the element symbol or the element symbol + a number. Coordinates are separated by spaces (Notice that the programming language PASCAL does not accept .137 or -.587. You always have to type the zeros: 0.137, -0.587). The default values for the coordination numbers are 4 for Si, Al, P and T, 2 for O and 0 for all the other elements. Examples: Si3 0.2348 0.4295 0.5 4 Na 0 0 0 P3 0.2373 0.2373 0.7667 5 2.2 Atoms ----- Specific atoms are designated by an atom label, the sequential number of the atom (in brackets) and the unit cell translation (in brackets). The command 'disc' shows the sequential numbers of all the symmetrically equivalent atoms in the unit cell. The default value for the sequential number is (1) and for the unit cell translation (0 0 0). (Only the first bracket is mandatory.) Examples: Si1 (3) (0 0 1) T2 Al3 (7) P2 ( 23 -1 -1 -1 Alternatively, the atom label and the symmetry operation, which transforms the original atom (with sequential number 1) to the desired atom, can be given. Examples: Si1 -X,-X+Y,-Z+1/2 AL5 -2X,-X,Z 2.3 Space groups ------------ The space groups are specified by their short symbols in Hermann-Mauguin notation. The bar operation is coded as '-' (either before or after the rotation axis symbol) and screw axes are given by two integers. Blank spaces are ignored. Examples: Ibam P 43 21 2 P N 3- N For the monoclinic system, space groups with different settings and cell choices are specified by their extended Hermann-Mauguin symbols. If the short symbol is given, the program assume the setting with the b-axis unique. (if this is not possible, the setting with the c-axis unique). Examples: Cm = C1m1, Im = I1m1, Bb = B11b 1For orthorhombic, tetragonal and cubic space groups with two different origin choices, the default is the first setting given in the International Tables [3]. To specify the choice of the origin, an additional character is appended to the space group symbol as follows: Z for origin at a center of symmetry Example: Fd-3mZ S for origin choice 1 of the International Tables [3] Example: Fd-3mS For trigonal space groups with rhombohedral symmetry, the program uses the rhombohedral axes by default. However, it is possible to specify the axis system explicitly with an additional character as follows: R for rhombohedral axes Example: R 3 m R H for hexagonal axis Example: R 3 m H The symmetry information of the space group is read from the file SYMDAT. Non-standard settings are calculated by transforming the symmetry operations of the standard ones. Other space groups can be added to the SYMDAT file. (see file description for SYMDAT) 3. Description of the commands =========================== 3.1 General ------- All commands can be written in capital or small letters. If a "display" command is given, but the required results have not yet been calculated, the necessary calculations are performed automatically. help displays a short summary of all commands. quit leaves the program. end leaves the program. 3.2 Crystal Structure and Distances ------------------------------- reacs reads the crystal structure data. The program asks for the compound identification code to read the structural data from an entry on the file STRUDAT. If you type , the data can be entered directly from the terminal. reafcs reads the crystal structure data from the first entry on the file STRUDAT. reancs reads next crystal structure data entry on the file STRUDAT. dise displays a list of the compound identification codes of all entries on the file STRUDAT. wrise writes a new entry for the present structure data on file STRUDATNEW. 1discs displays the crystal structure data: cell constants, space group, atom coordinates and symmetry constraints. diss displays the symmetry information of the space group. adda adds a new atom position. The program asks for a new atom position. (See 2.1) dela deletes an atom position. Enter the label of the atom position to be deleted. disc displays the sequential number, the coordinates and the symmetry constraints for all atoms in the unit cell. wrics writes the information displayed by discs on file LIST. wris writes the information displayed by diss on file LIST. wric writes the information displayed by disc on file LIST. cald calculates the 9 shortest distances from every given atom. (The number of bonds to be calculated can be changed in the constant declaration part of the source code before compilation.) disad displays all calculated distances. disd displays calculated distances from one atom disda displays the 7 shortest distances from every atom and the corresponding angles. disdv displays the calculated distances and the interatomic vectors of every atom. wrid writes the information displayed by disd on file LIST. wrida writes the information displayed by disda on file LIST. wridv writes the information displayed by disdv on file LIST. 3.3 Connectivity ------------ creab creates all bonds from the list of distances, starting with shortest distances. The number of bonds for an atom corresponds to the coordination number given for that atom. creb creates a bond between two given atoms. Enter the designations of the two atoms (see 2.2), or enter the designation of the first atom and the number of the distance (in the list of distances from the first atom obtained with the command 'disd'). delb deletes a bond between two atoms. Enter the designations of the two atoms (see 2.2), or enter the designation of the first atom and the number of the bond (in the list of bonds from the first atom obtained with the command 'disb'). NOTE: If you delete a bond, the numbering of the remaining bonds may 1 change. delab deletes all bonds. disb displays the bonds for one atom. disab displays the bonds for each atom. addo adds oxygen atoms by replacing the bonds between non-oxygen atoms with oxygen bridges. delo deletes all oxygen bridges and connects the non-oxygen atoms directly. wrib writes the information displayed by disb on file LIST. wriab writes the information displayed by disab on file LIST. 2.3 Topology -------- calcs calculates the first 10 values of the coordination sequence [4,5,6] for each atom position. dett determines the topology of the framework. The program deletes the oxygen bridges and connects the non-oxygen atoms directly. It then calculates the coordination sequences and compares them with coordination sequences of known frameworks [7] (contained on file COSEQ). callc calculates loop configurations [8]. The smallest rings that close each of the bond angles of each atom are calculated. This ring may not contain a third neighboring atom of the central atom. 3.4 Generation of input files ------------------------- wriid generates an input file for the program DLS-76 (with or without TETCON lines) and writes it on file DLSINPUT. If the number of bonds does not agree with the coordination number, the program asks you to change the coordination number to the number of bonds. wriil generates an input file for the program LOADAT of XRS-82 and writes it on file LOADATINPUT. If the number of bonds does not agree with the coordination number, the program asks you to change the coordination number to the number of bonds. 14. Description of the file structures ================================== 4.1 File SYMDAT ----------- The file SYMDAT contains the symmetry information of the different space goups. The entries have the following format: line n '============================' line n+1 '*', space group symbol (col. 2 - 22), space group number, code for the crystal system, code for center of symmetry line n+2ff symmetry operation last line '============================' The first character of the space group symbol must be the symbol of the centering type of cell (P,A,B,C,I,F,R). The code for the crystal system is - 'TRIC' for triclinic, - 'MON' for monoclinic, - 'ORT' for orthorhombic, - 'TET' for tetragonal, - 'TRIG' for trigonal with hexagonal axes, - 'RHO' for trigonal with rhombohedral axes, - 'HEX' for hexagonal and - 'CUB' for cubic. The code for the center of symmetry is -1 if a center of symmetry is at the origin, and 1 otherwise. Coordinates are separated by commas and fractions are written as two integers separated by a slash. For centered cells (A,B,C,I,F,R) only one of the positions related by centering needs to be given. If there is a center of symmetry at the origin and the code for the center of symmetry is -1, only one of the two centrosymmetric positions need to be given. Example: ======================================== *I4/MCM 140 TET -1 X,Y,Z X,-Y,Z+1/2 X,Y,-Z X,-Y,-Z+1/2 -Y,X,Z Y,X,Z+1/2 -Y,X,-Z Y,X,-Z+1/2 ======================================== In the file SYMDAT, non-standard settings are defined by a standard setting and a matrix (in brackets) which transforms the symmetry operations from the standard setting to the non-standard one. Examples: *P121 ==>P112(Y,Z,X) *PNNNS ==>PNNNZ(X-1/4,Y-1/4,Z-1/4) 14.2 File STRUDAT ------------ The file STRUDAT contains the crystal structures data. Every entry has a compound identification code. The entries have the following format: line n '----------------------------' line n+1 '*', compound identification code for this entry (col. 2 ...) line n+2 title line n+3 reference line n+4 space group symbol line n+5 cell parameters line n+7ff atom position last line '----------------------------' For the cell parameters, either all 6 values or just the independent ones can be given. Axial lengths are in angstroms and interaxial angles in degrees. For the specification of the space group and the atom positions see 2.3 and 2.1. Example: ------------------------------------- *abw Rubidium alumino-silicate Z. Krist.:142, 225-238 (1975). P c 21 n 9.22600 5.33700 8.74100 RB1 0.20370 0.50030 0.50090 SI1 0.08400 -0.01840 0.19390 4 AL1 0.41660 -0.01700 0.31280 4 O1 0.08480 -0.01760 0.01000 2 O2 -0.03110 -0.22470 0.25690 2 O3 0.03810 0.25660 0.25680 2 O4 0.24360 -0.09570 0.25350 2 ---------------------------------------- 4.3 File DISTDAT ------------ The file DISTDAT contains the prescribed values for the bond distances and angles, which are used to create the DISTAN, ANGLE and BONDIS cards in the input files of the programs DLS-76 and LOADAT. The entries have the following format: line n first element with coordination number, second element with coordination number, third element with coordination number (only for angles), prescribed value for this distance or angle, standard deviation Coordination numbers have to be given in square brackets. Example: SI[4] O [2] 1.628 0.01 AL[4] O [2] 1.740 0.01 SI[4] O [2] SI[4] 145 8.0 SI[4] O [2] AL[4] 145 8.0 O [2] SI[4] O [2] 109 2.0 O [1] AL[4] O [2] 109 2.0 14.4 File COSEQ ---------- The file COSEQ contains the coordination sequences of different frameworks. It is used to determine the structure type of a framework. The entries have the following format: line n code for the structure type, first 10 values of the coordination sequence, comment (optional) Example: ABW 4 10 21 36 54 78 106 136 173 214 AEL 4 11 21 37 59 85 114 150 189 232 AEL 4 11 22 38 58 85 115 148 188 234 AEL 4 12 24 40 59 84 115 150 186 230 AFG 4 10 20 34 53 76 103 135 170 208 AFG 4 10 20 34 54 78 104 134 168 210 AFI 4 11 21 35 53 77 105 137 172 212