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Information card for entry 5000095
Preview
| Coordinates | 5000095.cif |
|---|---|
| Original paper (by DOI) | HTML |
| Chemical name | Beryllium aluminium iron iron(III) magnesium aquasodium cyclo- hexasilicate * |
|---|---|
| Mineral name | Beryl |
| Formula | Al1.26 Be3 Fe0.32 H2.2 Mg0.42 Na0.45 O19.1 Si6 |
| Calculated formula | Al1.26 Be3 Fe0.32 H2.3833 Mg0.42 Na0.45 O19.1 Si6 |
| Title of publication | Single-crystal pulsed neutron diffraction of a highly hydrous beryl |
| Authors of publication | Artioli, G.; Rinaldi, R.; Wilson, C. C.; Zanazzi, P. F. |
| Journal of publication | Acta Crystallographica B (39,1983-) |
| Year of publication | 1995 |
| Journal volume | 51 |
| Journal issue | 5 |
| Pages of publication | 733 - 737 |
| a | 9.292 ± 0.001 Å |
| b | 9.292 ± 0.001 Å |
| c | 9.193 ± 0.001 Å |
| α | 90° |
| β | 90° |
| γ | 120° |
| Cell volume | 687.4 Å3 |
| Ambient diffraction temperature | 293 K |
| Number of distinct elements | 8 |
| Space group number | 192 |
| Hermann-Mauguin space group symbol | P 6/m c c |
| Hall space group symbol | -P 6 2c |
| Method of determination | single crystal |
| Diffraction radiation probe | x-ray |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 297042 (current) | 2025-01-02 | Added the '_diffrn_ambient_temperature', '_diffrn_radiation_probe' and '_cod_structure_determination_method' data items in entries 2101363, 5000095 after consulting the original publication. Removed the '_cod_duplicate_entry' data item from entry 5000095. |
5000095.cif |
| 188419 | 2016-11-14 | cif/5/00/00/ (antanas@kurmis) Marking entry 5000095 as a duplicate of entry 2101363. |
5000095.cif |
| 188417 | 2016-11-14 | cif/5/00/00/ Updating bibliography for entries 5000038, 5000095. |
5000095.cif |
| 176451 | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 5. |
5000095.cif |
| 130149 | 2015-01-27 | cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command. |
5000095.cif |
| 77586 | 2013-03-28 | cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(basename $i); C=$(echo $B|awk '{print "/home/saulius/struct/cod/cif/"substr($0,1,1)"/"substr($0,2,2)"/"substr($0,4,2)"/"$0}'); ( set -x; cif_merge --over \ _chemical_name_mineral,_chemical_name_structure_type,_chemical_name_common,_chemical_name_systematic,_chemical_formula_structural,_chemical_formula_sum \ $C $i ) \ | cif_filter --add-cif-header $C \ | sponge $C ) done in the working copy of the following repository: URL: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction/contributions Repository Root: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction Repository UUID: 9acf3947-1f02-0410-ae2a-984b57ad209b Revision: 2625 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 2625 Last Changed Date: 2013-03-28 15:13:00 +0200 (Thu, 28 Mar 2013) |
5000095.cif |
| 35911 | 2012-02-28 | cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree. |
5000095.cif |
| 966 | 2010-01-30 | cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated. |
5000095.cif |
| 858 | 2009-11-18 | cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \*.cif \ | xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ | ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ || ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ | ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ | ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ | awk '/^M/{print $NF}' \ | sort | xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst | xargs svn diff | less'), were reverted to the originals: cat only-reordered.lst | xargs svn revert Finally, a syntax check was performed using 'vcif': svn st | awk '/^M/{print $NF}' \ | sort | xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \*.cif \ | sort \ | xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st | grep '^M' | wc -l |
5000095.cif |
| 19 | 2008-01-26 | Changing all end-of-line codes from DOS style to UNIX style in all COD CIF files, for more convenient processing: In the cod/cif/ directory: ff \*.cif | xargs perl -i -pe 's/\r\n/\n/' |
5000095.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
5000095.cif |
| 13 | 2008-01-13 | Setting the svn:keywords property to "Author Date Revision URL Id" for all CIF files in the cod/cif directory. |
5000095.cif |
| 1 | 2007-11-30 | Adding all .cif files from the COD, downloaded in a Cod.zip file on 2007.02.07 (and the same Cod.zip is downloadable today, on 2007.11.29) |
5000095.cif |
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Users of the data should acknowledge the original authors of the
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