Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 9001554
Preview
| Coordinates | 9001554.cif |
|---|---|
| External links | AMCSD |
| Mineral name | Beryl |
|---|---|
| Formula | Al1.97 Be3 Fe0.03 H0.26 Na0.016 O18.24 Si6 |
| Calculated formula | Al1.97 Be3 Fe0.03 H0.26 Na0.016 O18.24 Si6 |
| Title of publication | Structure refinements of beryl by single-crystal neutron and X-ray diffraction Sample no. 2, aquamarine, probed with neutrons, T = 295 K |
| Authors of publication | Artioli, G.; Rinaldi, R.; Stahl, K.; Zanazzi, P. F. |
| Journal of publication | American Mineralogist |
| Year of publication | 1993 |
| Journal volume | 78 |
| Pages of publication | 762 - 768 |
| a | 9.218 Å |
| b | 9.218 Å |
| c | 9.197 Å |
| α | 90° |
| β | 90° |
| γ | 120° |
| Cell volume | 676.784 Å3 |
| Ambient diffraction temperature | 295 K |
| Number of distinct elements | 7 |
| Space group number | 192 |
| Hermann-Mauguin space group symbol | P 6/m c c |
| Hall space group symbol | -P 6 2c |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 283658 (current) | 2023-05-10 | cod/ (saulius@tasmanijos-velnias) Estimating atom types and attached hydrogen counts using the new cod-tools scripts [1], for those AMCSD files that had Wat or O-H or OW atoms, and where declared and computed formula matches after the update. Several files were spotted manually where attached hydrogen counts will need to be updated to match the title formula. The update command was: 553 ( set -x; directory-metadata; grep ^9 formula-with-estimated-atoms-all.tsv | grep = | awk '{print $1}' | sort -u | codid2file | xargs -i bash -c 'Z=$(cifvalues --no-dataname --tag _cell_formula_units_Z {}); if [ $Z = "?" ]; then NEW_Z=$(cif_estimate_Z {}); fi; cif_guess_AMCSD_atom_types {} | (if [ $Z = "?" -a -n "$NEW_Z" ]; then cif_select --invert --tag _cell_formula_units_Z | cat - <(echo _cell_formula_units_Z $NEW_Z); else cat; fi) | cif_filter --add-cif-header {} | sponge {}; echo Updated: {}'; date ) &> update-files-with-matching-formulae.log & run in the working copy of the repo [2]. Ref.: [1] saulius@tasmanijos-velnias COD/ $ svn info ~/src/cod-tools Path: /home/saulius/src/cod-tools Working Copy Root Path: /home/saulius/src/cod-tools URL: svn://cod.ibt.lt/cif-tools/trunk Relative URL: ^/trunk Repository Root: svn://cod.ibt.lt/cif-tools Repository UUID: 04be6746-3802-0410-999d-98508da1e98c Revision: 9577 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 9577 Last Changed Date: 2023-05-10 16:36:19 +0300 (Wed, 10 May 2023) [2] saulius@tasmanijos-velnias cod-entries-Wat-O-H-atoms/ $ svn info Path: . Working Copy Root Path: /home/saulius/tmp URL: svn+ssh://saulius.grazulis.lt/home/saulius/svn-repositories/tmp/COD/cod-entries-Wat-O-H-atoms Relative URL: ^/COD/cod-entries-Wat-O-H-atoms Repository Root: svn+ssh://saulius.grazulis.lt/home/saulius/svn-repositories/tmp Repository UUID: d3bd5daf-38a0-45fb-a3f8-6742599c9cef Revision: 580 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 580 Last Changed Date: 2023-05-06 10:43:38 +0300 (Sat, 06 May 2023) |
9001554.cif |
| 282068 | 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. |
9001554.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. |
9001554.cif |
| 176465 | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 9. |
9001554.cif |
| 85285 | 2013-05-05 | cod/ (saulius@koala.ibt.lt) Removing outdated _amcsd_database_code data items from all series 9 CIFs. |
9001554.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) |
9001554.cif |
| 35913 | 2012-02-28 | cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised. |
9001554.cif |
| 1210 | 2010-06-10 | cif/9/ Updating 13213 AMCSD CIFs, taking new data from the AMCSD database and adding the assigned AMCSD numbers. |
9001554.cif |
| 1071 | 2010-04-10 | cif/9/ Updating COD entries from AMCSD, processed in the AMCSD-resynchronisation-2009.06.24/ directory. Entries are updated if they could be unambiguously mapped to a unique COD number by automatic search scripts in AMCSD-resynchronisation-2009.06.24/. |
9001554.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. |
9001554.cif |
| 893 | 2009-11-20 | cif/ Generating _diffrn_ambient_temperature and _diffrn_ambient_pressure tags from the CIF file comments like "T = 100K" (using the 975 revision of cif_create_AMCSD_pressure_temp_tags). Mostly, series 9 CIFs (obtained AMCSD) have such comments. Only files that did not had these tags originally were changed. The tags were generated using the following command: ( \ set -x; \ find $(/bin/ls -rd ?) -name \*.cif \ | xargs -n1 -iX \ bash -c 'awk "/^#/,/^data_/{print}/^data_/{exit}" X \ | grep -v "^data_" > tmp-$$; \ cif_create_AMCSD_pressure_temp_tags X >> tmp-$$; \ if (grep -q _diffrn_ambient_temperature tmp-$$ >& /dev/null && \ ! grep -q _diffrn_ambient_temperature X >& /dev/null) || \ (grep -q _diffrn_ambient_pressure tmp-$$ >& /dev/null && \ ! grep -q _diffrn_ambient_pressure X >& /dev/null); \ then \ mv -v tmp-$$ X; \ fi; \ rm -f tmp-$$' \ ) >& make-temp-pressure-tags.log After this, the modified files were checked using 'vcif': svn st | grep ^M | awk '{print $NF}' | xargs -n1 vcif -l 2048 It was checked that for the other tags, only tag order and value formatting has changed in the modifed files, if at all: ( \ set -x; \ svn st ? \ | awk '/^M/{print $NF}' \ | sort \ | xargs -n1 -iX \ bash -c 'echo -e "\n"=== X ===; \ diff -b \ <(svn cat X | sort) \ <(sort X)' \ ) 2>&1 | tee diff-sorted.log tdbgrep === diff-sorted.log \ | grep -v ^=== \ | grep -v '^> _diffrn_' \ | grep . \ | grep -vE '^[0-9]+a[0-9]+' \ | less and the changed files were validated against the cif_core.dic (thus checking, among others checks, that the values of the inserted tags have correct types): ( \ set -x; \ svn st ? \ | awk '/^M/{print $NF}' \ | sort \ | xargs -n1 -iX \ bash -c 'echo === X ===; \ cif_validate \ --dic ~/struct/CIF-dictionaries/cif_core.dic \ X \ --check-all \ --do-not-check-tag-exists-local' \ ) >& validate-pressure-temperature.log |
9001554.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 |
9001554.cif |
| 255 | 2008-03-10 | Redepositing all AMCSD (9*series) COD CIF files. This redeposition regenerates AMCSD (9* series) files, 10011 entries total, from the original source CIF file cifdata.cif found on the CD received from Armel. Most importantly, the truncated formulas seem to be corrected. The files are not folded, i.e. they have lines longer than 80 characters (conforming CIF 1.1 specification, but not CIF 1.0 specification), and are otherwise syntactically correct. Some missing coordinates were fixed manually, restoring them from the AMCSD site, and non-ASCII symbols were fixed automatically during filtering. After the redeposition, the cifs-with-errors.lst was regenerated using the following command: find -name \*.cif \ | xargs -n1 -iI sh -c 'vcif -l 2048 I || echo I' \ | grep -vE 'CIF|ERR' \ | sort > cifs-with-errors.lst & |
9001554.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/' |
9001554.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
9001554.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. |
9001554.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) |
9001554.cif |
All data in the COD and the database itself are dedicated to the
public domain and licensed under the
CC0
License
.
Users of the data should acknowledge the original authors of the
structural data.