SADIAN91 Manual scanned in from hard copy by Lachlan Cranswick (lachlan@melbpc.org.au) Melbourne, Australia, 2nd March, 1997. Using Mustek MFS-8000SP Scanner and Lynx OCR Character Recognition Software for MS-Windows 95. "Although this DOS verion is officially labeled a "test version" it should run properly on all platforms and for all applications. Please read the file readme.txt" ************************************* This is a test version. Please, inform of any errors or suggest improvements. ******* SADIAN91 ******* LAST REV. Jan. 3, 1991 Written by W. H. Baur, G. Wenninger and R. D. Roy at UIC. R. X. Fischer inserted the Burzlaff symmetry routine. D. Kassner wrote the symmetry analysis parts including the DLS-input routine and rearranged and cleaned up the program in order to make the FORTRAN text easier to understand. This is the VAX(and PC) - version. Please, quote as: W.H. Baur and D. Kassner: Sadian90 prepares input for DLS-76 (and does other things as well. Z. Krist. Suppl. Issue, No. 3, 15 (1991)) SADIAN is a program which Searches for Atomic DIstances and ANgles in crystal structures. It searches for all interatomic distances and/or bond angles within a specified number of unit cells surrounding the reference unit cell, up to spe- cified limits. It prepares sketches in the three main directions and calculates polar coordinates around any atom (for the construction of ball and spoke mo- dels). It writes two files: a. a file containing the proper input for the DLS-76 program (Baerlocher, Hepp and Meier, 1977) The DLS input generator determines the distances of neigh- boring atoms and prints them in DLS-76 format. Redundant symmetry related distances are eliminated. SYMEQ inputs are generated as needed. Special equi- valent positions are recognized and the proper constraints printed with the coordinates. You may have to edit the file in order to get a simulation cor- responding to your own prejudices. b. another file contains all the other output of the program (SAD.OUT or *.SLS when using the PC-version). Details of the input: 1) Title card (20A4): columns 1 - 80 may contain any desired identification. 2) Control Card (F10.7,5I3,F10.7,5I3,4F5.2,3I1): Columns: 1-10 DMAX: Limit up to which distances are printed out (in Angstrom). When DMAX=O, calculation of interatomic distances is bypassed, and no dis- tance tables are printed. Keep DMAX reasonably small when trying for a DLS input file which should run immediately, without editing, in DLS. 11-13 NA: number of atoms in asymmetric unit (<500). 14-16 NT: number of translations: =1 for P, =2 for C or I, =4 for F, =1 for rhombohedral, =3 for trigonal. 17-19 NS: number of symmetry positions (<= 48). For noncentrosymmetric structures NS is egual to the number of equivalent points of the general position divided by NT. For centrosymmetric structures it is one-half this number. 20-22 NCENT: =1 if there is a symmetry center at the origin of the unit cell; =2 otherwise. 23-25 NW: =O if no bond angles are to be calculated, = -1 if bond angles are to be calculated around all atoms, when CA-A and CA-B, the sides of the angles, are smaller than AMX. If NW >O, NW=total number of the angle control cards for the atoms around which bond angles will be calculated, in case one wishes to know the bond angles around selected atoms only (NW<=NA). (See input 7.) 26-35 AMX: Limit for the sides of the angles to be calculated (in Angstroms). When AMX is given as a negative value, not only A-CA-B, but also the angles CA-A-B and CA-B-A will be computed. 36-38 IDR: = 1 if standard deviations are to be calculated. War- ning: in tetragonal, trigonal, hexagonal and cubic space groups, the calculated e.s.d.'s will differ sometimes for symmetry equivalent bonds and angles around an atom in a special position: the highest e.s.d. is the correct one. If IDR=O, no e.s.d.'s are calculated. 39-41 NCL: (<8) specifies the number of cells (linear) which will be searched for distances and angles. The parameters listed on the atomic parameter cards are normalized in such a way that they assume positions in a central reference unit cell. The search is then performed within NCL**3 unit cells. If NCL is left blank, the default is 3, so that 27 unit cells are searched. 42-44 NDRA: = 1 if sketches are to be made. 45-47 NPOL: = 1 if polar coordinates are to be calculated. 48-50 IDENS: number of spaces per atom lable (in DRAW) 51-55 SCAL: Scale for orthogonal coordinates of drawing. If scale is made negative all three sketches will be on one scale, if positive, each one will be as large as the paper allows. 56-60 BBO: bottom bound of drawing (DRAW) 61-65 TBO: top bound of drawing (DRAW) 66-70 FCOF: size reduction of sketch (DRAW) 71 IWRITE: identifies modes of output: = O (=default): output is full (sketches for lineprinter, complete tables of coordinates for sketch; expanded distance and angle tables, useful for debugging purposes); = 1: compressed tabularoutput, but full-size sketches; = 2: 79-column output with length/width ratio suitable for IBM terminal; = 3: 79-column output with proper ratio for VT320 terminal (VAX). 72 ISKTCH: = O (default): duplicate sketches are suppressed. = 1: no suppression of sketches. 73 IBURZ: = O (default): symmetry input as described below. = 1: replaces symmetry section by one line containing Hermann-Maugin symbol (max. 45 char). There should be blanks between the different parts of the symbol. When IBURZ=1 entries NT (cols. 14-16), NS (cols. 17-19) and NCENT (cols. 20-22) are ignored. The setting, description and choice of origin correspond to the entries in the International Tab les for X-ray Crystallography, vol. 1. If the Tables have entries for two different choices of origin always that one is chosen for which the inversion center is at the origin. Rhombohedral space groups (R) are al ways given in the hexagonal setting. The space group symbol can be gi- ven in the short or the long form. The routine should correctly inter- pret many non-standard settings, such as Ic (instead of Cc). It will fail on some, possibly because of problems with the choice of origin. 74,75 IDLS: = O (default): file SAD.DLS is not written; > O (maximum=21): file SAD.DLS with DLS-76 input is written. IDLS is internally decremented by one, so that IDLS-1 = number of lines containing prescribed distances etc., which have to be added at the end, see input 8). 3) Cell constant card (3F10.4,3F10.6) Columns: 1-10,11-20,21-30: a, b, c cell edges in angstroms or inverse angstroms 31-40,41-50,51-60: alpha, beta, gamma (in degrees) or cosines of the angles, or reciprocal angles; 90 can be left as blank. 4) Atomic parameter cards (A4,26X,3F10.6), not more than 500. Columns: 1-4 Atom label 7-30 Irrelevant to SADIAN 31-40 Fractional x coordinate of the atom 41-50 Fractional y coordinate of the atom 51-60 Fractional z coordinate of the atom 61-66 Standard deviation for x 67-72 Standard deviation for y 73-78 Standard deviation for z The format is the same as in BLFLS. Output of BLFLS could be used here, x, y and z may have any value: they can be negative or greater than one. The para- meters are normalized so that they lie within the reference unit cell. 5) Translation card (3F1O.8), not more than 8. Columns: 1-10,11-20,21-30: Tx, Ty, Tz: translation in the x, y, z directions expressed as fractions of the respective cell edges, corresponding to the centering of non-primitive lattices. For primitive lattice a blank card has to be submitted. [Called ANT(I,J) inside the program. ] 6) symmetry cards (3(F15.9,3F3.0)), not more than 48. This must correspond to the general equivalent position if you want the DLS part to work correctly. For the SADIAN part you can use shortcuts. ((TTS(I,J),(TS(K,I,J),K=1,3),I=1,3),J=1,NS) Columns: 1-15,25-39.49-63: Translational parts of the expression for the equivalent position, in directions x, y, z. 16-18,19-21,22-24: multipliers of x, y and z for x' 40-42,43-45.46-48: multipliers of x, y and z for y'. 64-66,67-69,70-72: multipliers of x, y and z for z'. The format is the same as in the BNL version of BLFLS. The definitions of x', y' and z' are: x' = TTSx + (TSx)(l)*x + (TSx)(2)*y + (TSx)(3)*z Y' = TTSy + (TSy)(l)*x + (TSy)(2)*y + (TSy)(3)*z z' = TTSz + (TSz)(l)*x + (TSz)(2)*y + (TSz)(3)*z 7) Angle control cards (F6.3, 22I3), optional. necessary only if NW>O. 1-6 AMAX, same as AMX, but applies to atom # given in cols. 7-9 7-9 CA, # of central atom around which angles are computed 10-12 CN=O, all angles around CA are calculated CN>O, # of atoms used in angle calculations, enumerated in COAT (CN<21). 13-15, COAT, numbers of coordinated atoms, as for CA these are the 16-18, consecutive numbers in the atom list. etc. till 70-72 8) Prescribed distances and their weights for DLS-output (2(A4,X),4F10.5) 1-4 LT1, Label of atom type 1 ) upper and lower case are different 6-9 LTZ, Label of atom type 2 ) watch out, in comparing label in 4) 11-20 CD, Central distance for searching for potential prescribed distances in SADIAN when preparing DLS-input 21-30 RN, range around CD 31-40 PD, prescribed distance to be used in DLS 41-50 WP, weight of prescribed distance to be used in DLS LT1 and LT2 must correspond to the alphabetic characters of the atom label of the atomic parameter cards 4). Numbers in the labels of cards 4) are ignored. All distances within CD plus/minus RN in the SADIAN distance tables are taken as prescribed distances for the DLS-input and are given PD as the prescribed distance and WP as its assigned weight. Interatomic distances between any two atoms identified by LT1 and LT2 (and within the DMAX range allowed by SADIAN), but outside of CD +/- RN, show up in the DLS input with a weight of 0.001, that is they are listed with the bond lengths calculated by SADIAN, but do not contribute strongly to the DLS-model. Distances not defined at all by a pair of LT1 and LT2 labels are treated the same way. Properly chosen parameters LT1, LT2, CD, RN, PD, WP and DMAX (s. card 2) usually result in a DLS input file which can be used without any editing immediately for a DLS run. Actually useless distances are mostly generated by too generous a choice (that is too large a value) of DMAX on Control Card 2.