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package Demeter::UI::Artemis::Data::BondValence;
=for Copyright
.
Copyright (c) 2006-2019 Bruce Ravel (http://bruceravel.github.io/home).
All rights reserved.
.
This file is free software; you can redistribute it and/or
modify it under the same terms as Perl itself. See The Perl
Artistic License.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
=cut
use strict;
use warnings;
use Chemistry::Elements qw(get_symbol);
use Demeter::UI::Wx::SpecialCharacters qw($S02);
use Demeter::UI::Wx::Colours;
use List::MoreUtils qw(any uniq);
use Scalar::Util qw(looks_like_number);
use Statistics::Descriptive;
use Xray::BondValence qw(bvdescribe valences available);
use Wx qw( :everything );
use base qw(Wx::Dialog);
use Wx::Event qw(EVT_LISTBOX EVT_BUTTON EVT_RADIOBOX EVT_CHOICE);
use Wx::Perl::TextValidator;
sub new {
my ($class, $parent, @paths) = @_;
my $this = $class->SUPER::new($parent, -1, "Artemis: Compute a bond valence sum",
Wx::GetMousePosition, wxDefaultSize,
wxMINIMIZE_BOX|wxCAPTION|wxSYSTEM_MENU|wxSTAY_ON_TOP
);
my $vbox = Wx::BoxSizer->new( wxVERTICAL );
## --- elements and valences
my $gbs = Wx::GridBagSizer->new( 6, 10 );
$vbox -> Add($gbs, 0, wxGROW|wxALL, 5);
my $abs = get_symbol($paths[0]->bvabs);
$gbs -> Add( Wx::StaticText -> new($this, -1, $abs.' valence:'), Wx::GBPosition->new(0,0));
$this->{valence_abs} = Wx::Choice -> new($this, -1, wxDefaultPosition, wxDefaultSize, [valences($abs)]);
$gbs -> Add( $this->{valence_abs}, Wx::GBPosition->new(0,1));
my %unique;
foreach my $p (@paths) {
++$unique{$p->bvscat};
};
my $i = 0;
foreach my $s (sort keys %unique) {
my $ss = get_symbol($s);
$gbs -> Add( Wx::StaticText -> new($this, -1, $ss.' valence:'), Wx::GBPosition->new($i,3));
my @list = uniq map {(split(/:/, $_))[3]} available($abs, '.', $s); # find possible valences for scatterer
$this->{"valence_scat$ss"} = Wx::Choice -> new($this, -1, wxDefaultPosition, wxDefaultSize, [@list]);
$gbs -> Add( $this->{"valence_scat$ss"}, Wx::GBPosition->new($i,4));
++$i;
};
## --- s02 value
my $hbox = Wx::BoxSizer->new ( wxHORIZONTAL );
$vbox -> Add($hbox, 0, wxGROW|wxALL, 0);
$hbox -> Add(Wx::StaticText->new($this, -1, $S02.":"), 0, wxGROW|wxALL, 5);
$this->{s02} = Wx::TextCtrl->new($this, -1, "1");
$this->{s02} -> SetValidator( Wx::Perl::TextValidator->new( qr([0-9.]) ) );
$hbox -> Add($this->{s02}, 0, wxGROW|wxALL, 5);
## --- compute button
$this->{compute} = Wx::Button->new($this, -1, 'Compute');
$vbox -> Add($this->{compute}, 0, wxGROW|wxALL, 5);
EVT_BUTTON($this, $this->{compute}, sub{OnCompute(@_, @paths)});
## --- result
$hbox = Wx::BoxSizer->new ( wxHORIZONTAL );
$vbox -> Add($hbox, 0, wxGROW|wxALL, 0);
$hbox -> Add(Wx::StaticText->new($this, -1, "Bond valence sum:"), 0, wxGROW|wxALL, 5);
$this->{bvs} = Wx::TextCtrl->new($this, -1, q{}, wxDefaultPosition, wxDefaultSize, wxTE_READONLY);
$hbox -> Add($this->{bvs}, 0, wxGROW|wxALL, 5);
## --- feedback
my $fbbox = Wx::StaticBox->new($this, -1, 'Feedback', wxDefaultPosition, wxDefaultSize);
my $fbboxsizer = Wx::StaticBoxSizer->new( $fbbox, wxVERTICAL );
$this->{feedback} = Wx::TextCtrl->new($this, -1, q{}, wxDefaultPosition, [120, 200], wxTE_MULTILINE|wxTE_READONLY);
$fbboxsizer -> Add($this->{feedback}, 1, wxGROW|wxALL, 0);
$vbox -> Add($fbboxsizer, 1, wxGROW|wxLEFT|wxRIGHT, 5);
## --- document button
$this->{doc} = Wx::Button->new($this, -1, q{Docmentation: BVS}, wxDefaultPosition, wxDefaultSize, 0, );
$vbox -> Add($this->{doc}, 0, wxGROW|wxALL, 5);
EVT_BUTTON($this, $this->{doc}, sub{$::app->document('extended.bvs')});
## --- OK button
$this->{ok} = Wx::Button->new($this, wxID_OK, q{}, wxDefaultPosition, wxDefaultSize, 0, );
$vbox -> Add($this->{ok}, 0, wxGROW|wxALL, 5);
$this -> SetSizerAndFit( $vbox );
return $this;
};
sub OnCompute {
my ($this, $event, @paths) = @_;
my $s02 = $this->{s02}->GetValue;
return if not looks_like_number($s02);
my $color = Wx::TextAttr->new(Wx::Colour->new('#550000'), $wxBGC,
Wx::Font->new(9, wxTELETYPE, wxNORMAL, wxBOLD, 0, "" ) );
my $sum = 0;
foreach my $p (@paths) {
$p->_update("fft");
$p->valence_abs($this->{valence_abs}->GetStringSelection);
$p->valence_scat($this->{"valence_scat".$p->bvscat}->GetStringSelection);
my @found = available($p);
if ($#found == -1) {
my $text = sprintf("Bond valence parameters are not available for the combination of %s %d and %s %d",
$p->bvabs, $p->valence_abs, $p->bvscat, $p->valence_scat);
$this->{feedback}->SetValue($text);
$this->{feedback}->SetStyle(0, $this->{feedback} -> GetLastPosition, $color);
return;
};
$sum += $p->bv($s02);
};
$this->{bvs}->SetValue(sprintf("%.3f", $sum));
my %seen;
my $text = "Bond valence parameters:\n";
foreach my $p (@paths) {
next if $seen{$p->bvscat};
$text .= " ".bvdescribe($p).$/;
++$seen{$p->bvscat};
};
$this->{feedback}->SetValue($text);
$this->{feedback}->SetInsertionPointEnd;
$text = "\n" . $this->sanity_path_too_long(@paths) . "\n\n";
$text .= $this->sanity_paths_split_shells(@paths) . "\n\n";
$text .= $this->sanity_ms_paths(@paths) . "\n";
if ($text !~ m{\A\s*\z}) {
my $was = $this->{feedback} -> GetInsertionPoint;
$this->{feedback}->AppendText($text);
$this->{feedback}->SetStyle($was, $this->{feedback} -> GetInsertionPoint, $color);
};
};
sub sanity_path_too_long {
my ($this, @paths) = @_;
if (any {$_->R > 2.5} @paths) {
return "Some paths are longer than 2.5A. Bond valence sums are only valid on paths in the first coordination shell.";
};
return q{};
};
sub sanity_paths_split_shells {
my ($this, @paths) = @_;
return q{} if $#paths < 1;
my $stat = Statistics::Descriptive::Full->new();
foreach my $p (@paths) {
$stat->add_data($p->R);
};
if ($stat->standard_deviation > 0.2) {
return "The standard deviation of your paths is larger than 0.2A. A bond valence sum should only include paths in the first coordination shell.";
};
return q{};
};
sub sanity_ms_paths {
my ($this, @paths) = @_;
if (any {$_->nleg > 2} @paths) {
return "Some paths are multiple scattering paths. Bond valence sums should use only single scattering paths.";
};
return q{};
};
1;
=head1 NAME
Demeter::UI::Artemis::Data::BondValence - Dialog to perform a simple bond valence sum calculation
=head1 VERSION
This documentation refers to Demeter version 0.9.26.
=head1 SYNOPSIS
This module provides a dialog for computing a bond valence sum using a
set of marked paths and table of bond valence parameters maintained by
I. David Brown of McMaster University.
=head1 DEPENDENCIES
Demeter's dependencies are in the F<Build.PL> file.
=head1 BUGS AND LIMITATIONS
Please report problems to the Ifeffit Mailing List
(L<http://cars9.uchicago.edu/mailman/listinfo/ifeffit/>)
Patches are welcome.
=head1 AUTHOR
Bruce Ravel, L<http://bruceravel.github.io/home>
L<http://bruceravel.github.io/demeter/>
=head1 LICENCE AND COPYRIGHT
Copyright (c) 2006-2019 Bruce Ravel (L<http://bruceravel.github.io/home>). All rights reserved.
This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself. See L<perlgpl>.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
The tabulation of bond valence parameters carried the following
copyright notice and disclaimer:
#***************************************************************
# COPYRIGHT NOTICE
# This table may be used and distributed without fee for
# non-profit purposes providing
# 1) that this copyright notice is included and
# 2) no fee is charged for the table and
# 3) details any changes made in this list by anyone other than
# the copyright owner are suitably noted in the _audit_update record
# Please consult the copyright owner regarding any other uses.
#
# The copyright is owned by I. David Brown, Brockhouse Institute for
# Materials Research, McMaster University, Hamilton, Ontario Canada.
# idbrown@mcmaster.ca
#
#*****************************DISCLAIMER************************
#
# The values reported here are taken from the literature and
# other sources and the author does not warrant their correctness
# nor accept any responsibility for errors. Users are advised to
# consult the primary sources.
#
#***************************************************************
=cut
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