============================================================================== K R I B E R : U S E R M A N U A L Version 1.0 (January 1991) ============================================================================== 5. Worked example ============== This example shows the generation of a DLS-input file from structure data estimated from a physical model. The file STRUDAT contains the following entry. --------------- *EXAMPLE example data from model R -3 m H 13.3 23.0 T1 0.0 0.22 0.05 T2 0.22 0.0 0.5 --------------- For clarity , the commands entered from the keyboard are written in capitel letters, and additional comments are preceded by an exclamation mark. ****************************************************************************** * * * Program KRIBER Version 1.0 (January 1991) * * =============== * * * * an interactive PASCAL program to * * - calculate distances and angles * * - generate input files for the programs DLS-76 and LOADAT (XRS-82) * * - calculate coordination squences and loop configurations * * * * Author: Roland Bialek, Institut fuer Kristallografie und Petrografie * * ETH-Z, CH-8092 Zuerich, Switzerland * * * * ===> type help to get a summary of the commands * * quit or exit to leave the program * * * ****************************************************************************** ===>REACS Enter compound identification code to read data from the file STRUDAT or to enter the data interactively:EXAMPLE ... entry EXAMPLE found ! The structure data were read from the file STRUDAT ===>DISCS Name: example Lit: data from model 1 Cell parameters: a = 13.300 b = 13.300 c = 23.000 alpha = 90.000 beta = 90.000 gamma = 120.000 Space group: R -3 M H Atoms with coordination number and atoms per unit cell ( 1) T1 ( 0.0000 0.2200 0.0500) 4 36 X,Y,Z ( 2) T2 ( 0.2200 0.0000 0.5000) 4 18 X,0,+1/2 ===>DISAD Distances from atom T1 ( 1)( 0 0 0) to (1) - T1 ( 11)( 0 0-1) 2.3000 (2) - T1 ( 4)(-1 0 0) 2.9260 (3) - T1 ( 6)( 0 0 0) 2.9260 (4) - T1 ( 9)(-1 0-1) 3.7218 (5) - T1 ( 8)( 0 0-1) 3.7218 (6) - T2 ( 9)( 0 0 0) 3.7439 (7) - T2 ( 10)( 0 0 0) 4.7516 (8) - T1 ( 2)(-1-1 0) 5.0680 (9) - T1 ( 3)( 0 0 0) 5.0680 Distances from atom T2 ( 1)( 0 0 0) to (1) - T2 ( 4)( 0-1 0) 2.9260 (2) - T2 ( 5)( 0 0 0) 2.9260 (3) - T1 ( 23)( 0-1 0) 3.7439 (4) - T1 ( 26)( 0 0 0) 3.7439 (5) - T1 ( 28)( 0 0 0) 4.7516 (6) - T1 ( 21)( 0-1 0) 4.7516 (7) - T2 ( 3)(-1-1 0) 5.0680 (8) - T2 ( 2)( 0 0 0) 5.0680 (9) - T1 ( 13)( 0-1 0) 5.6258 ! The list of distances shows that distances no. 4, 5 and 6 from ! atom T1 have nearly the the same length. Because rough coordinates ! were used, distances 4 and 5 from atom T1 are too short. ===>DISAB ... new bond T1 ( 1)( 0 0 0) -- T1 ( 11)( 0 0-1) created ... new bond T1 ( 1)( 0 0 0) -- T1 ( 4)(-1 0 0) created ... new bond T1 ( 1)( 0 0 0) -- T1 ( 6)( 0 0 0) created ... new bond T1 ( 1)( 0 0 0) -- T1 ( 9)(-1 0-1) created WARNING too many bonds for T1 ... new bond T2 ( 1)( 0 0 0) -- T2 ( 4)( 0-1 0) created ... new bond T2 ( 1)( 0 0 0) -- T1 ( 23)( 0-1 0) created WARNING too many bonds for T1 Bonds from atom T1 ( 1)( 0 0 0) (1) - T1 ( 11)( 0 0-1) 2.3000 (2) - T1 ( 4)(-1 0 0) 2.9260 (3) - T1 ( 6)( 0 0 0) 2.9260 (4) - T1 ( 9)(-1 0-1) 3.7218 (5) - T1 ( 8)( 0 0-1) 3.7218 symm. equival. to bond (4) (6) - T2 ( 9)( 0 0 0) 3.7439 Bonds from atom T2 ( 1)( 0 0 0) (1) - T2 ( 4)( 0-1 0) 2.9260 (2) - T2 ( 5)( 0 0 0) 2.9260 symm. equival. to bond (1) (3) - T1 ( 23)( 0-1 0) 3.7439 (4) - T1 ( 26)( 0 0 0) 3.7439 symm. equival. to bond (3) 1 ! The program tries to find 4 bonds for both atoms T1 and T2 from ! the calculated distances. Because the distances 4 and 5 form the ! atom T1 are symmetrically equivalent, generation of bond no. 4 ! results in the generation of a fifth bond for this atom. This ! gives a bond number, which is greater than the coordination number. ! A WARNING message is written. Generation of the bond no. 4 for the ! atom T2 results in a sixth bond for atom T1. A second WARNING ! message is written. ===>DELB Delete bond: first atom:T1 second atom or bond no. (from disb):4 ... old bond T1 ( 1)( 0 0 0) -- T1 ( 9)(-1 0-1) broken ! With the command "delb" the wrong bond no. 4 can be deleted (since ! no. 5 is symmetrically equivalent to no. 4, it is also deleted), ! to get the correct connection. ===>DISAB Bonds from atom T1 ( 1)( 0 0 0) (1) - T1 ( 11)( 0 0-1) 2.3000 (2) - T1 ( 4)(-1 0 0) 2.9260 (3) - T1 ( 6)( 0 0 0) 2.9260 (4) - T2 ( 9)( 0 0 0) 3.7439 Bonds from atom T2 ( 1)( 0 0 0) (1) - T2 ( 4)( 0-1 0) 2.9260 (2) - T2 ( 5)( 0 0 0) 2.9260 symm. equival. to bond (1) (3) - T1 ( 23)( 0-1 0) 3.7439 (4) - T1 ( 26)( 0 0 0) 3.7439 symm. equival. to bond (3) ===>ADDO ... old bond T1 ( 1)( 0 0 0) -- T1 ( 11)( 0 0-1) broken ... new bond T1 ( 1)( 0 0 0) -- O1 ( 1)( 0 0 0) created ... old bond T1 ( 1)( 0 0 0) -- T1 ( 6)( 0 0 0) broken ... new bond T1 ( 1)( 0 0 0) -- O2 ( 1)( 0 0 0) created ... old bond T1 ( 1)( 0 0 0) -- T1 ( 4)(-1 0 0) broken ... new bond T1 ( 1)( 0 0 0) -- O3 ( 1)(-1 0 0) created ... old bond T1 ( 1)( 0 0 0) -- T2 ( 9)( 0 0 0) broken ... new bond T1 ( 1)( 0 0 0) -- O4 ( 1)( 0 0 0) created ... new bond T2 ( 9)( 0 0 0) -- O4 ( 1)( 0 0 0) created ... old bond T2 ( 1)( 0 0 0) -- T2 ( 4)( 0-1 0) broken ... new bond T2 ( 1)( 0 0 0) -- O5 ( 1)( 0-1 0) created ! Oxygen atoms are added to form the oxygen bridges. Now the input ! file for the program DLS-76 can be generated. ===>WRIID DLSinput with TETCON cards? (y/n):Y ! The following calculation of the coordination sequence and the ! loop configuration is a test for the correct connectivity. First ! the oxygen bridges are removed, and non-oxygen atom are connected ! directly. ===>DETT ... old bond O5 ( 1)( 0 0 0) -- T2 ( 4)( 0 0 0) broken ... new bond T2 ( 1)( 0 1 0) -- T2 ( 4)( 0 0 0) created ... old bond O4 ( 1)( 0 0 0) -- T2 ( 9)( 0 0 0) broken 1... old bond O4 ( 1)( 0 0 0) -- T1 ( 1)( 0 0 0) broken ... new bond T1 ( 1)( 0 0 0) -- T2 ( 9)( 0 0 0) created ... old bond O3 ( 1)( 0 0 0) -- T1 ( 4)( 0 0 0) broken ... new bond T1 ( 1)( 1 0 0) -- T1 ( 4)( 0 0 0) created ... old bond O2 ( 1)( 0 0 0) -- T1 ( 6)( 0 0 0) broken ... new bond T1 ( 1)( 0 0 0) -- T1 ( 6)( 0 0 0) created ... old bond O1 ( 1)( 0 0 0) -- T1 ( 11)( 0 0-1) broken ... new bond T1 ( 1)( 0 0 0) -- T1 ( 11)( 0 0-1) created Coordination sequences: T1 4 9 17 30 49 71 92 114 143 183 T2 4 10 20 32 46 64 90 124 156 184 Possible frameworks: T1 LEV T2 LEV ===>CALLC Loop configuration for T1 ( 1)( 0 0 0) Angle T1 ( 4) -- T1 ( 1) -- T2 ( 9) has 1 loop with 6 atoms - T1 ( 1)( 0 0 0) T2 ( 9)( 0 0 0) T1 ( 34)(-1 0 0) T1 ( 31)(-1 0 0) T2 ( 11)(-1-1 0) T1 ( 4)(-1 0 0) Angle T1 ( 6) -- T1 ( 1) -- T2 ( 9) has 1 loop with 4 atoms - T1 ( 1)( 0 0 0) T2 ( 9)( 0 0 0) T2 ( 10)( 0 0 0) T1 ( 6)( 0 0 0) Angle T1 ( 6) -- T1 ( 1) -- T1 ( 4) has 2 loops with 6 atoms - T1 ( 1)( 0 0 0) T1 ( 4)(-1 0 0) T1 ( 2)(-1-1 0) T1 ( 5)( 0-1 0) T1 ( 3)( 0 0 0) T1 ( 6)( 0 0 0) - T1 ( 1)( 0 0 0) T1 ( 4)(-1 0 0) T1 ( 9)(-1 0-1) T1 ( 11)( 0 0-1) T1 ( 8)( 0 0-1) T1 ( 6)( 0 0 0) Angle T1 ( 11) -- T1 ( 1) -- T2 ( 9) has 1 loop with 6 atoms - T1 ( 1)( 0 0 0) T2 ( 9)( 0 0 0) T2 ( 10)( 0 0 0) T1 ( 6)( 0 0 0) T1 ( 8)( 0 0-1) T1 ( 11)( 0 0-1) Angle T1 ( 11) -- T1 ( 1) -- T1 ( 4) has 1 loop with 4 atoms - T1 ( 1)( 0 0 0) T1 ( 4)(-1 0 0) T1 ( 9)(-1 0-1) T1 ( 11)( 0 0-1) Angle T1 ( 11) -- T1 ( 1) -- T1 ( 6) has 1 loop with 4 atoms - T1 ( 1)( 0 0 0) T1 ( 6)( 0 0 0) T1 ( 8)( 0 0-1) T1 ( 11)( 0 0-1) Loop configuration for T2 ( 1)( 0 0 0) Angle T2 ( 5) -- T2 ( 1) -- T2 ( 4) has 1 loop with 6 atoms - T2 ( 1)( 0 0 0) T2 ( 4)( 0-1 0) T2 ( 3)(-1-1 0) T2 ( 6)(-1 0 0) T2 ( 2)( 0 0 0) T2 ( 5)( 0 0 0) Angle T1 ( 23) -- T2 ( 1) -- T2 ( 4) has 1 loop with 4 atoms - T2 ( 1)( 0 0 0) T2 ( 4)( 0-1 0) T1 ( 21)( 0-1 0) T1 ( 23)( 0-1 0) Angle T1 ( 23) -- T2 ( 1) -- T2 ( 5) has 3 loops with 8 atoms - T2 ( 1)( 0 0 0) T2 ( 5)( 0 0 0) T1 ( 28)( 0 0 0) T1 ( 26)( 0 0 0) T1 ( 29)( 0 0 0) T2 ( 6)( 0 0 0) T1 ( 20)( 0-1 0) T1 ( 23)( 0-1 0) - T2 ( 1)( 0 0 0) T2 ( 5)( 0 0 0) T2 ( 2)( 0 0 0) T2 ( 6)(-1 0 0) T2 ( 3)(-1-1 0) T2 ( 4)( 0-1 0) T1 ( 21)( 0-1 0) T1 ( 23)( 0-1 0) - T2 ( 1)( 0 0 0) T2 ( 5)( 0 0 0) T1 ( 19)( 0 0 0) T1 ( 17)( 0 0 0) T2 ( 18)( 0 0 0) T2 ( 15)( 0 0 0) T1 ( 13)( 0-1 0) T1 ( 23)( 0-1 0) 1 Angle T1 ( 26) -- T2 ( 1) -- T2 ( 4) has 3 loops with 8 atoms - T2 ( 1)( 0 0 0) T2 ( 4)( 0-1 0) T1 ( 21)( 0-1 0) T1 ( 23)( 0-1 0) T1 ( 20)( 0-1 0) T2 ( 6)( 0 0 0) T1 ( 29)( 0 0 0) T1 ( 26)( 0 0 0) - T2 ( 1)( 0 0 0) T2 ( 4)( 0-1 0) T2 ( 3)(-1-1 0) T2 ( 6)(-1 0 0) T2 ( 2)( 0 0 0) T2 ( 5)( 0 0 0) T1 ( 28)( 0 0 0) T1 ( 26)( 0 0 0) - T2 ( 1)( 0 0 0) T2 ( 4)( 0-1 0) T1 ( 30)(-1-1 0) T1 ( 32)(-1-1 0) T2 ( 12)( 0-1 0) T2 ( 8)( 0-1 0) T1 ( 36)( 0 0 0) T1 ( 26)( 0 0 0) Angle T1 ( 26) -- T2 ( 1) -- T2 ( 5) has 1 loop with 4 atoms - T2 ( 1)( 0 0 0) T2 ( 5)( 0 0 0) T1 ( 28)( 0 0 0) T1 ( 26)( 0 0 0) Angle T1 ( 26) -- T2 ( 1) -- T1 ( 23) has 1 loop with 6 atoms - T2 ( 1)( 0 0 0) T1 ( 23)( 0-1 0) T1 ( 20)( 0-1 0) T2 ( 6)( 0 0 0) T1 ( 29)( 0 0 0) T1 ( 26)( 0 0 0) ===>QUIT ****************************************************************************** * end of program KRIBER * ****************************************************************************** On file DLSINPUT are the following lines: TITLE example DLS-76 1 10 2 0 2 1 CELL HEX 13.3000 13.3000 23.0000 90.0000 90.0000 120.00 ATOM T1 0.00000 0.22000 0.05000 T X,Y,Z ATOM T2 0.22000 0.00000 0.50000 T X,0,+1/2 ATOM O1 0.00000 0.21991 0.00000 O 0,Y,0 ATOM O2 0.10969 0.21938 0.05023 O X,2X,Z ATOM O3 0.89053 0.10947 0.04957 O -Y+1,Y,Z ATOM O4 0.05625 0.33358 0.10880 O X,Y,Z ATOM O5 0.11053 0.88947 0.50047 O -Y+1,Y,Z SYMEQ T1 T1*A -X,-X+Y,-Z SYMEQ T1 T1*B -X+Y,Y,Z SYMEQ T1 T1*C -Y,-X,Z SYMEQ T1 T1*D -X+1/3,-X+Y-1/3,-Z+2/3 SYMEQ T1 T1*E -Y+2/3,X-Y+1/3,Z+1/3 SYMEQ T2 T2*A -X+Y+1/3,-X+2/3,Z-1/3 SYMEQ T2 T2*B -Y,-X,Z SYMEQ T2 T2*C X,X-Y,Z SYMEQ O3 O3*A X-1,Y,Z SYMEQ O4 O4*A -X+1/3,-X+Y-1/3,-Z+2/3 SYMEQ O4 O4*B -Y+2/3,X-Y+1/3,Z+1/3 SYMEQ O5 O5*A X,Y-1,Z SYMEQ O5 O5*B X-Y+1,X,-Z+1 BONDIS T O T 1.62800 -0.00040 0.00000 145.00000 2.0 0.4 0.2 TETCON T1 O1 O2 O3*A O4 T1*A T1*B T1*C T2*A TETCON T2 O4*A O4*B O5*A O5*B T1*D T1*E T2*B T2*C END FINISH