Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 9006139
Preview
| Coordinates | 9006139.cif |
|---|
| Mineral name | Pentlandite |
|---|---|
| Formula | Fe4.23 Ni4.77 S8 |
| Calculated formula | Fe4.23 Ni4.77 S8 |
| Title of publication | Cation distribution in Pentlandites (Fe,Ni)9S8: dependence of pressure and temperature and kinetics of the cation exchange reaction Sample: Natural, Fe/(Fe+Ni) = .470, T = 423 K, P = 0 GPa Note: structure was not refined in this study |
| Authors of publication | Tsukimura K; Nakazawa H; Endo T; Fukunaga O |
| Journal of publication | Physics and Chemistry of Minerals |
| Year of publication | 1992 |
| Journal volume | 19 |
| Pages of publication | 203 - 212 |
| a | 10.095 Å |
| b | 10.095 Å |
| c | 10.095 Å |
| α | 90° |
| β | 90° |
| γ | 90° |
| Cell volume | 1028.77 Å3 |
| Ambient diffraction temperature | 423 K |
| Ambient diffracton pressure | 0 kPa |
| Number of distinct elements | 3 |
| Space group number | 225 |
| Hermann-Mauguin space group symbol | F m -3 m |
| Hall space group symbol | -F 4 2 3 |
| Duplicate of | 9006138 |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 291455 (current) | 2024-05-02 | Inserting missing Z values into entries of range 9 |
9006139.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. |
9006139.cif |
| 112050 | 2014-04-29 | cod/ (saulius@koala.ibt.lt) Marking 392 files as duplicates of the COD entries (with smaller COD IDs) that had identical title, cell constants and coordinates: mysql -u cod_reader cod -e ' select d1.file, d2.file from data as d1 join data as d2 on ( d1.title = d2.title or d1.title = substr(d2.title,1,length(d2.title)-1) or d2.title = substr(d1.title,1,length(d1.title)-1)) and d1.file < d2.file and d1.a = d2.a and d1.b = d2.b and d1.c = d2.c and d1.vol = d2.vol and (d1.calcformula = d2.calcformula or d1.calcformula is null or d2.calcformula is null) and d1.duplicateof is null and d2.duplicateof is null and d1.optimal is null and d2.optimal is null order by d1.file, d2.file' -NB \ | xargs -i bash -c ' F1=$(echo {} | awk "{print \$1}" | codid2file); F2=$(echo {} | awk "{print \$2}"| codid2file); true echo === {} ===; if diff -q <(cif2ref $F1) <(cif2ref $F2) >& /dev/null; then CODID=$(echo {} | awk "{print \$1}"); echo $CODID is the main entry for $F2; echo "_cod_duplicate_entry $CODID" >> $F2; fi' The localhost `cod` database's table `data` was loaded with the last night's COD `data` dump. |
9006139.cif |
| 77586 | 2013-03-28 | cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(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) |
9006139.cif |
| 35913 | 2012-02-28 | cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised. |
9006139.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. |
9006139.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 |
9006139.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 |
9006139.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. |
9006139.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 & |
9006139.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/' |
9006139.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
9006139.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. |
9006139.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) |
9006139.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.