---
name: "cif_find_duplicates"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_find_duplicates"
---

# cif\_find\_duplicates(1)

find COD numbers for the .cif files in given directories of file lists.

## NAME

cif\_find\_duplicates - find COD numbers for the .cif files in given directories of file lists.

## SYNOPSIS

cif\_find\_duplicates --options my-cif-dir1/ my-cif-dir2/files\*.cif COD-cif-dir/

## DESCRIPTION

Find COD numbers for the .cif files in given directories of file lists.

## OPTIONS

\-c, --always-continue\
                   Continue processing and return successful return status\
                   even if errors are diagnosed.

\-c-, --always-die\
                   Stop and return error status if errors are diagnosed.

\--max-cell-length-difference 0.5\
                   Maximum difference of unit cell lengths allowed for\
                   entries regarded as the same, in angstroms\
                   (default: 0.5).

\--max-cell-angle-difference 1.2\
                   Maximum difference of unit cell angles allowed for\
                   entries regarded as the same, in angstroms\
                   (default: 1.2).

\--check-bibliography\
                   Only CIFs that have different bibliography data are\
                   declared different if all other parameters match.\
                   CIFs with missing bibliographies are assumed to have\
                   matching bibliographies (default).

\--no-check-bibliography, --dont-check-bibliography\
                   Ignore bibliographic data of all CIFs; thus even files\
                   with different bibliographies will be regarded the same\
                   if their cells, chemical formulae and measurement\
                   conditions match.

\--use-sigma, --dont-ignore-sigma, --no-ignore-sigma\
                   Use standard deviations (sigmas) when comparing unit\
                   cell constants (default).

\--no-use-sigma, --dont-use-sigma, --ignore-sigma\
                   Ignore standard uncertainties (sigmas) when comparing\
                   unit cell constants.

\--check-sample-history\
                   Only CIFs that have different sample history data\
                   (as recorded in the \_exptl\_crystal\_thermal\_history\
                   and \_exptl\_crystal\_pressure\_history tags) are declared\
                   different if all other parameters match.

\--no-check-sample-history,

\--dont-check-sample-history,

\--disregard-sample-history\
                   Ignore sample history of all CIFs; thus even files\
                   with different sample histories will be regarded the\
                   same if their cells, chemical formulae and measurement\
                   conditions match (default).

\--use-attached-hydrogens\
                   Include the number of implicit hydrogen atoms\
                   when calculating the summary chemical formula.\
                   Implicit hydrogen atoms are specified using\
                   the \_atom\_site\_attached\_hydrogens data item.

\--no-use-attached-hydrogens,

\--ignore-attached-hydrogens\
                   Ignore the number of implicit hydrogen atoms\
                   when calculating the summary chemical formula.\
                   Implicit hydrogen atoms are specified using\
                   the \_atom\_site\_attached\_hydrogens data item\
                   (default).

\--continue-on-errors\
                   Do not terminate script if errors are raised.

\--die-on-errors, --dont-continue-on-errors,

\--do-not-continue-on-errors, --no-continue-on-errors\
                   Terminate script immediately if errors are raised (default).

\--continue-on-warnings\
                   Do not terminate script if warnings are raised (default).

\--die-on-warnings\
                   Terminate script immediately if warnings are raised.

\--continue-on-notes\
                   Do not terminate script if notes are raised (default).

\--die-on-notes\
                   Terminate script immediately if notes are raised.

\--use-perl-parser\
                   Use Perl parser to parse CIF files.

\--use-c-parser\
                   Use C parser to parse CIF files (default).

\--help, --usage\
                   Output a short usage message (this message) and exit.

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cif\_find\_duplicates bugs using e-mail: cod-bugs@ibt.lt