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.