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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2022-07-31 09:41:50 +0300 (Sun, 31 Jul 2022) $
#$Revision: 9352 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cif_reduce_cell $
#------------------------------------------------------------------------------
#*
#* Perform reductions of the unit cell using different algorithms.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use File::Basename qw( basename );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Data qw( get_cell );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::CIF::Tags::Manage qw( set_tag );
use COD::CIF::Tags::Print qw( print_cif );
use COD::Cell::Niggli::KG76;
use COD::Cell::Delaunay::Delaunay;
use COD::SOptions qw( getOptions get_value );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( process_warnings
process_errors
process_parser_messages );
use COD::ToolsVersion qw( get_version_string );
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $base0 = basename( $0 );
my $use_parser = 'c';
my $debug = 0;
my $epsilon = 1E-4;
# Default formats for floating-point numbers (for unit cell
# parameters) -- large enough for IEEE double precision floating point
# number:
my $cell_fformat = "%.12g";
my $Pi = 4 * atan2(1,1);
#* OPTIONS:
#* --use-perl-parser
#* Use Perl parser for CIF parsing.
#* --use-c-parser
#* Use Perl & C parser for CIF parsing (default).
#*
#* -F, --float-format "%15.12f"
#* Specify format to print out floating point numbers.
#*
#* -C, --cell-format "%15.12f"
#* Specify format to print out floating point numbers for
#* atomic coordinates.
#*
#* -e, --epsilon 1E-6
#* Tolerance to compare cell parameter equality in cell
#* reductions.
#*
#* --debug, --no-debug
#* Turn on/off the debug prints of reduction algorithm.
#* Default: off.
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
"--debug" => sub{ $debug = 1 },
"--no-debug" => sub{ $debug = 0 },
"-e,--epsilon" => \$epsilon,
"-F,--float-format" => sub { $cell_fformat = get_value() },
"-C,--cell-format" => \$cell_fformat,
"--use-perl-parser" => sub { $use_parser = "perl" },
"--use-c-parser" => sub { $use_parser = "c" },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print get_version_string(), "\n"; exit }
);
@ARGV = ( "-" ) unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
for my $filename (@ARGV) {
my $options = { 'parser' => $use_parser, 'no_print' => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
process_parser_messages( $messages, $die_on_error_level );
next if $err_count > 0;
canonicalize_all_names( $data );
for my $datablock (@$data) {
my $values = $datablock->{values};
my $dataname = 'data_' . $datablock->{'name'};
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level )
};
eval {
my @cell = get_cell( $values );
# Niggli reduction:
use COD::Cell::Niggli::KG76;
$COD::Cell::Niggli::KG76::debug = $debug;
my @Niggli_cell =
COD::Cell::Niggli::KG76::reduce( @cell, $epsilon );
my $tag_prefix = "_[local]_Niggli_${base0}";
set_tag( $datablock, $tag_prefix."_length_a",
sprintf( $cell_fformat, $Niggli_cell[0] ));
set_tag( $datablock, $tag_prefix."_length_b",
sprintf( $cell_fformat, $Niggli_cell[1] ));
set_tag( $datablock, $tag_prefix."_length_c",
sprintf( $cell_fformat, $Niggli_cell[2] ));
set_tag( $datablock, $tag_prefix."_angle_alpha",
sprintf( $cell_fformat, $Niggli_cell[3] ));
set_tag( $datablock, $tag_prefix."_angle_beta",
sprintf( $cell_fformat, $Niggli_cell[4] ));
set_tag( $datablock, $tag_prefix."_angle_gamma",
sprintf( $cell_fformat, $Niggli_cell[5] ));
# Delaunay reduction:
use COD::Cell::Delaunay::Delaunay qw(reduce);
$COD::Cell::Delaunay::Delaunay::debug = $debug;
my @Delaunay_cell =
COD::Cell::Delaunay::Delaunay::reduce( @cell, $epsilon );
$tag_prefix = "_[local]_Delaunay_${base0}";
set_tag( $datablock, $tag_prefix."_length_a",
sprintf( $cell_fformat, $Delaunay_cell[0] ));
set_tag( $datablock, $tag_prefix."_length_b",
sprintf( $cell_fformat, $Delaunay_cell[1] ));
set_tag( $datablock, $tag_prefix."_length_c",
sprintf( $cell_fformat, $Delaunay_cell[2] ));
set_tag( $datablock, $tag_prefix."_angle_alpha",
sprintf( $cell_fformat, $Delaunay_cell[3] ));
set_tag( $datablock, $tag_prefix."_angle_beta",
sprintf( $cell_fformat, $Delaunay_cell[4] ));
set_tag( $datablock, $tag_prefix."_angle_gamma",
sprintf( $cell_fformat, $Delaunay_cell[5] ));
# Estimate conventional cell:
use COD::Cell::Conventional::deWG91 qw(conventional_cell);
$COD::Cell::Conventional::deWG91::debug = $debug;
my @primitive_cell = @Niggli_cell[0..5];
my @conventional_cell = conventional_cell( @primitive_cell, $epsilon );
$tag_prefix = "_[local]_Niggli_conv_${base0}";
set_tag( $datablock, $tag_prefix."_length_a",
sprintf( $cell_fformat, $conventional_cell[0] ));
set_tag( $datablock, $tag_prefix."_length_b",
sprintf( $cell_fformat, $conventional_cell[1] ));
set_tag( $datablock, $tag_prefix."_length_c",
sprintf( $cell_fformat, $conventional_cell[2] ));
set_tag( $datablock, $tag_prefix."_angle_alpha",
sprintf( $cell_fformat, $conventional_cell[3] ));
set_tag( $datablock, $tag_prefix."_angle_beta",
sprintf( $cell_fformat, $conventional_cell[4] ));
set_tag( $datablock, $tag_prefix."_angle_gamma",
sprintf( $cell_fformat, $conventional_cell[5] ));
set_tag( $datablock, $tag_prefix."_crystal_system",
$conventional_cell[7] );
# Print out CIF data:
$COD::CIF::Tags::Print::max_cif_tag_len = 46;
print_cif( $datablock,
{
preserve_loop_order => 1,
keep_tag_order => 1
}
);
};
if ($@) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level->{'ERROR'} );
}
}
}
|
