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Information card for entry 1000007
Preview
| Coordinates | 1000007.cif |
|---|---|
| Original paper (by DOI) | HTML |
| External links | AMCSD |
| Mineral name | Diopside |
|---|---|
| Formula | Ca Mg O6 Si2 |
| Calculated formula | Ca4 Mg4 O24 Si8 |
| Title of publication | The crystal structure of diopside at pressure to 10 GPa Sample: P = 1 atm |
| Authors of publication | Thompson, R. M.; Downs, R. T. |
| Journal of publication | American Mineralogist |
| Year of publication | 2008 |
| Journal volume | 93 |
| Pages of publication | 177 - 186 |
| a | 9.7397 Å |
| b | 8.9174 Å |
| c | 5.2503 Å |
| α | 90° |
| β | 105.866° |
| γ | 90° |
| Cell volume | 438.631 Å3 |
| Ambient diffracton pressure | 100 kPa |
| Number of distinct elements | 4 |
| Space group number | 15 |
| Hermann-Mauguin space group symbol | C 1 2/c 1 |
| Hall space group symbol | -C 2yc |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 282068 (current) | 2023-03-26 | cod/ (saulius@tasmanijos-velnias) Adding the '_cod_related_entry_...' loop to those COD AMCSD entries that lacked it, and adding the related AMCSD database ID to this loop. |
1000007.cif |
| 282053 | 2023-03-24 | cod/ (saulius@tasmanijos-velnias) Updating the existing COD records from the recent AMCSD downloads: - Adding AMCSD IDs to those COD records that exacly matched the AMCSD structures (comparing unit cells, space groups, coordinates and measurement conditions) but did not yet have the AMCSD ID; - Adding new mineral names, compound sources, measurement conditions (when those were missing) and other informations from the AMCSD CIFs. |
1000007.cif |
| 278219 | 2022-09-27 | cif/1/00/00/ Added an explicit space group operation list based on the provided space group symbols and updated space group information using the 'cif_filter' program in entries 1000007-1000013. |
1000007.cif |
| 176435 | 2016-02-14 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries from ranges 1, 2. |
1000007.cif |
| 120071 | 2014-07-11 | Adding DOIs to range 1 structures. | 1000007.cif |
| 85284 | 2013-05-05 | cif/ (saulius@koala.ibt.lt) Removing the _amcsd_database_code from the series 1 CIFs, since the the assigments of AMCSD in COD are outdated. |
1000007.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 $C ) done in the working copy of the following repository: URL: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction/contributions Repository Root: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction Repository UUID: 9acf3947-1f02-0410-ae2a-984b57ad209b Revision: 2625 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 2625 Last Changed Date: 2013-03-28 15:13:00 +0200 (Thu, 28 Mar 2013) |
1000007.cif |
| 35911 | 2012-02-28 | cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree. |
1000007.cif |
| 1212 | 2010-06-10 | cif/ Inserting AMCSD numbers for the automatically recognised series 1, 2, 4, 5 and 8 CIFs. |
1000007.cif |
| 1140 | 2010-05-02 | cif/1/ Merging values from the new AMCSD data (AMCSD-resynchronisation-2009.06.24/) into 1000007.cif. |
1000007.cif |
| 1082 | 2010-04-11 | cif/1/ Updating bibliography in the series 1 CIFs from the AMCSD-resynchronisation-2009.06.24/ directory: for i in outputs/redeposit/1*.cif ; \ do ( \ B=$(basename $i); \ C=~/struct/cod/cif/1/$B; \ echo === Updating $C ===; \ cif_filter --bibliography $i --add-cif-header $C $C > tmp; \ /bin/mv tmp $C \ ) done |
1000007.cif |
| 966 | 2010-01-30 | cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated. |
1000007.cif |
| 900 | 2009-11-21 | cif/ Renaming data blocks of all COD CIFs so that they have COD number (taken from the COD file name) as their datablock number: find ? -name \*.cif \ | xargs \ perl \ -MFile::Basename \ -i \ -lpe 's/^data_([^\s]*)/"data_".basename($ARGV, ".cif")/e' After this change, 'cif2cod' will give correct keys in the generated table. Also, data block names are guaranteed to be distinct, so any subset of COD CIFs can be concatenated into one file without introducing ambiguity. |
1000007.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 $NF}' \ | sort | xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \*.cif \ | sort \ | xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X || { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st | grep '^M' | wc -l |
1000007.cif |
| 853 | 2009-11-16 | cif/ Reconstructing spacegroup designators from the symmetry operators were possible. The comands used can be found in the log file reformat-spacegroups-2009.11.14.log committed with the current revision. Only lines that contained spacegroup designators were changed, and all files pass vcif test after the conversion. |
1000007.cif |
| 618 | 2009-04-13 | Changing tag _chemical_name into _chemical_name_mineral in 11 series 1* CIFs. |
1000007.cif |
| 20 | 2008-01-26 | Removing white space at the end of all lines from all COD CIF files: in the cod/cif/ directory: ff \*.cif | xargs perl -i -pe 's/\s+\n$/\n/' |
1000007.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/' |
1000007.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
1000007.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. |
1000007.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) |
1000007.cif |
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