The platon crystallographic package
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- Bu səhifədəki naviqasiya:
- A-I.3 - The SHELX Style RES Format
- A-I.4 - CIF-DATA FORMAT
- APPENDIX III - SPACE GROUP SYMMETRY
- APPENDIX IV - Radii Used in PLATON
- A-IV.2 – Van der Waals Radii
programs. Scaling the data to Angstrom scale will be necessary to obtain connected sets with a PLOT instruction. ATOM cards may be as simple as: C1 1.123 1.456 1.789. A-I.3 - The SHELX Style RES Format SHELX type files are recognized as well. Atomic parameters should be preceded with an FVAR card since this triggers the program to expect SHELX format input. An END card on a SHELX file will be ignored. A-I.4 - CIF-DATA FORMAT A restricted format CIF-DATA file (such as produced by SHELXL-97) is acceptable. Appendix II - Recognized Reflection File Data Formats Preferably a SHELXL97 FCF style reflection file should be provided where relevant and possible. Several variations of Fo/Fc files produced with non-SHELXL software packages are recognized as well. In addition SHELXL-97 style HKLF3 & HKLF4 reflection files are recognized along with those associated with a number of other packages. Notes: − When PLATON is invoked with a CIF file it will automatically search for a file with the same name and extension .fcf. When such a file is not found, it will search for a file with .hkl extension. − When PLATON is invoked with a .ins or .res file, it will search for a corresponding .hkl file. − The data names in the CIF and FCF files should be identical. The same applies for the cell dimensions. − PLATON works out the reflection file type from the content and not from the file extension. APPENDIX III - SPACE GROUP SYMMETRY Space group symmetry is handled in PLATON with a general space group symmetry handling routine that manages all symmetry operations. This routine permits the space group symmetry to be specified either explicitly in terms of the general equivalent positions listed in the International Tables or implicitly in terms of a small set of space group generators from which the complete set of symmetry operators is set up. The generators for all space groups in their standard setting and many commonly used non-standard settings are also implicitly retrievable by the program from internal tables on the basis of the specified name of the space group (e.g. R-3m) , either in Hermann-Mauguin or Hall format. The Hall symbol (Hall, 1981) allows for the complete specification of the generators, including those for alternative settings. PLATON assumes in the absence of any symmetry information, contrary to SHELXL, a non-centrosymmetric primitive lattice. Example: The symmetry for space group number 19 (P2 1 2 1 2 1 ) may be specified in PLATON either as: SHELX/RES Style: LATT -1 SYMM 1/2 + X, 1/2 - Y, -Z SYMM -X, 1/2 + Y, 1/2 – Z SYMM 1/2 - X, - Y, 1/2 + Z PLATON/SPF Style: LATT P A SYMM X, Y, Z SYMM 1/2 + X, 1/2 - Y, -Z SYMM -X, 1/2 + Y, 1/2 - Z SYMM 1/2 - X, - Y, 1/2 + Z or LATT P A SYMM 1/2 + X, 1/2 - Y, -Z SYMM -X, 1/2 + Y, 1/2 - Z or SPGR P212121 (or HALL 'P 2ac 2ab') A LATT card, when present, should precede any SYMM card in order that the symmetry arrays are initialized to either, by default, a primitive non-centrosymmetric lattice or to the specified lattice type: (P/A/B/C/I/F) and (A)Centric type (A/C). The general equivalent positions should be given as specified in International Tables and preferably should have the centre of symmetry at the origin when the space group is centro- symmetric. The symmetry operation SYMM X,Y,Z is always implicitly assumed as the first symmetry operation and needs not be given although any redundancy in the symmetry input will be ignored. Rhombohedral lattice types in the hexagonal setting should be specified explicitly as LATT R and in the rhombohedral setting as LATT P. Thus the generators for space group R3 in hexagonal setting are: LATT R A SYMM -Y, X-Y, Z and in the rhombohedral setting (Specified as: R3r): LATT P A SYMM Z, X, Y The translational part may be specified either as a ratio or as a real (e.g. 1/4 or 0.25). Monoclinic-b is taken as the standard setting for monoclinic space groups. Other settings are to be specified by the full space group name: e.g. P112 for the monoclinic-c setting of P2. Non-standard orthorhombic settings such as space group A2aa may be handled by specifying Ccc2 -cba on the SPGR card (see International Tables Vol A) where Ccc2 is the standard setting and '-cba' the axial transformation. In fact the program automatically modifies the input line accordingly for non-standard settings. The standard setting symmetry is than transformed accordingly. APPENDIX IV - Radii Used in PLATON A-IV.1 – Atomic Radii used for covalent bonding etc. Ac 1.88 Er 1.73 Na 0.97 Sb 1.46 Ag 1.59 Eu 1.99 Nb 1.48 Sc 1.44 Al 1.35 F 0.64 Nd 1.81 Se 1.22 Am 1.51 Fe 1.35 Ni 1.50 Si 1.20 As 1.21 Ga 1.22 Np 1.55 Sm 1.80 Au 1.50 Gd 1.79 O 0.68 Sn 1.65 B 0.83 Ge 1.27 Os 1.50 Sr 1.12 Ba 1.34 H 0.35 P 1.05 Ta 1.43 Be 0.35 Hf 1.57 Pa 1.61 Tb 1.76 Bi 1.72 Hg 1.70 Pb 1.97 Tc 1.35 Br 1.21 Ho 1.74 Pd 1.50 Te 1.49 C 0.68 I 1.40 Pm 1.80 Th 1.79 Ca 0.99 In 1.63 Po 1.68 Ti 1.47 Cd 1.69 Ir 1.32 Pr 1.82 Tl 1.64 Ce 1.83 K 1.33 Pt 1.50 Tm 1.72 Cl 0.99 La 1.87 Pu 1.53 U 1.75 Co 1.23 Li 0.68 Ra 1.90 V 1.33 Cr 1.35 Lu 1.72 Rb 1.47 W 1.37 Cs 1.67 Mg 1.10 Re 1.60 Y 1.78 Cu 1.52 Mn 1.35 Rh 1.45 Yb 1.94 D 0.23 Mo 1.47 Ru 1.50 Zn 1.45 Dy 1.75 N 0.68 S 1.04 Zr 1.56 Notes: - The covalent radii come from various sources - HW & D are equivalent to H, OW is equivalent to O and Q1 is equivalent to C1. A-IV.2 – Van der Waals Radii Ac -2.68 Er -2.53 Na 2.27 Sb -2.26 Ag 1.72 Eu -2.79 Nb -2.28 Sc -2.24 Al -2.15 F 1.47 Nd -2.61 Se 1.90 Am -2.31 Fe -2.14 Ni 1.63 Si 2.10 As 1.85 Ga 1.87 Np -2.35 Sm -2.60 Au 1.66 Gd -2.59 O 1.52 Sn 2.17 B -1.63 Ge -1.97 Os -2.17 Sr -1.92 Ba -2.14 H 1.20 P 1.80 Ta -2.23 Be -1.15 Hf -2.37 Pa -2.41 Tb -2.56 Bi -2.34 Hg 1.55 Pb 2.02 Tc -2.15 Br 1.85 Ho -2.54 Pd 1.63 Te 2.06 C 1.70 I 1.98 Pm -2.60 Th -2.59 Yüklə 5,01 Kb. Dostları ilə paylaş:
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