← Back to branch summary

~ubuntu-branches/ubuntu/intrepid/horae/intrepid

« back to all changes in this revision

Viewing changes to artemis_parts/atoms2.pl

  • Committer: Bazaar Package Importer
  • Author(s): Carlo Segre
  • Date: 2008-02-23 23:13:02 UTC
  • mfrom: (2.1.2 hardy)
  • Revision ID: james.westby@ubuntu.com-20080223231302-mnyyxs3icvrus4ke
Tags: 066-3
Apply patch to athena_parts/misc.pl for compatibility with 
perl-tk 804.28.

Show diffs side-by-side

added added

removed removed

Lines of Context:
artemis_parts/atoms2.pl
10
10
 
11
11
  $atoms_params{edge} = 'K';
12
12
  $atoms_params{elem} = 'H';
13
 
  my @help_button = (-foreground=>$config{colors}{activehighlightcolor},
14
 
                     -font=>$config{fonts}{small},
15
 
                     -relief=>'flat', -borderwidth=>0,
16
 
                     -activeforeground=>$config{colors}{mbutton},
 
13
  my @help_button = (-foreground       => $config{colors}{activehighlightcolor},
 
14
                     -font             => $config{fonts}{small},
 
15
                     -relief           => 'flat',
 
16
                     -borderwidth      => 0,
 
17
                     -cursor           => $mouse_over_cursor,
 
18
                     -activeforeground => $config{colors}{mbutton},
17
19
                    );
18
20
 
19
21
  my $fr = $atoms -> LabFrame(-label=>'Titles',
45
47
  $fr -> Button(@help_button,
46
48
                -text=>'Space group', -command=>[\&Echo, $click_help{'Space group'}])
47
49
    -> grid(-column=>0, -row=>0, -sticky=>'e', -padx=>2, -pady=>2);
48
 
  $widgets{atoms_space} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
50
  $widgets{atoms_space} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
49
51
                                       -validate=>'key',
50
52
                                       -validatecommand=>[\&set_atoms_params, 'space'])
51
53
    -> grid(-column=>1, -row=>0, -padx=>2, -pady=>2);
54
56
  ## lattice constants
55
57
  $fr -> Button(@help_button, -text=>'A', -command=>[\&Echo, $click_help{'A'}])
56
58
    -> grid(-column=>0, -row=>1, -sticky=>'e', -padx=>2);
57
 
  $widgets{atoms_a} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
59
  $widgets{atoms_a} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
58
60
                                   -validate=>'key',
59
61
                                   -validatecommand=>[\&set_atoms_params, 'a'])
60
62
    -> grid(-column=>1, -row=>1);
61
63
  $fr -> Button(@help_button, -text=>'B', -command=>[\&Echo, $click_help{'B'}])
62
64
    -> grid(-column=>0, -row=>2, -sticky=>'e', -padx=>2);
63
 
  $widgets{atoms_b} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
65
  $widgets{atoms_b} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
64
66
                                   -validate=>'key',
65
67
                                   -validatecommand=>[\&set_atoms_params, 'b'])
66
68
    -> grid(-column=>1, -row=>2);
67
69
  $fr -> Button(@help_button, -text=>'C', -command=>[\&Echo, $click_help{'C'}])
68
70
    -> grid(-column=>0, -row=>3, -sticky=>'e', -padx=>2);
69
 
  $widgets{atoms_c} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
71
  $widgets{atoms_c} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
70
72
                                   -validate=>'key',
71
73
                                   -validatecommand=>[\&set_atoms_params, 'c'])
72
74
    -> grid(-column=>1, -row=>3);
74
76
  ## lattice angles
75
77
  $fr -> Button(@help_button, -text=>'Alpha', -command=>[\&Echo, $click_help{'Alpha'}])
76
78
    -> grid(-column=>0, -row=>4, -sticky=>'e', -padx=>2);
77
 
  $widgets{atoms_alpha} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
79
  $widgets{atoms_alpha} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
78
80
                                       -validate=>'key',
79
81
                                       -validatecommand=>[\&set_atoms_params, 'alpha'])
80
82
    -> grid(-column=>1, -row=>4);
81
83
  $fr -> Button(@help_button, -text=>'Beta', -command=>[\&Echo, $click_help{'Beta'}])
82
84
    -> grid(-column=>0, -row=>5, -sticky=>'e', -padx=>2);
83
 
  $widgets{atoms_beta} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
85
  $widgets{atoms_beta} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
84
86
                                      -validate=>'key',
85
87
                                      -validatecommand=>[\&set_atoms_params, 'beta'])
86
88
    -> grid(-column=>1, -row=>5);
87
89
  $fr -> Button(@help_button, -text=>'Gamma', -command=>[\&Echo, $click_help{'Gamma'}])
88
90
    -> grid(-column=>0, -row=>6, -sticky=>'e', -padx=>2);
89
 
  $widgets{atoms_gamma} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
91
  $widgets{atoms_gamma} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
90
92
                                       -validate=>'key',
91
93
                                       -validatecommand=>[\&set_atoms_params, 'gamma'])
92
94
    -> grid(-column=>1, -row=>6);
97
99
  $fr -> Button(@help_button,
98
100
                -text=>'Cluster size', -command=>[\&Echo, $click_help{'Cluster size'}])
99
101
    -> grid(-column=>0, -row=>7, -sticky=>'e', -padx=>2, -pady=>2);
100
 
  $widgets{atoms_rmax} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
102
  $widgets{atoms_rmax} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
101
103
                                      -validate=>'key',
102
104
                                      -validatecommand=>[\&set_atoms_params, 'rmax'])
103
105
    -> grid(-column=>1, -row=>7, -padx=>2);
115
117
  $fr -> Button(@help_button,
116
118
                -text=>'Shift vector', -command=>[\&Echo, $click_help{'Shift vector'}])
117
119
    -> grid(-column=>0, -row=>9, -sticky=>'e', -padx=>2);
118
 
  $widgets{atoms_shiftx} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
120
  $widgets{atoms_shiftx} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
119
121
                                        -validate=>'key',
120
122
                                        -validatecommand=>[\&set_atoms_params, 'shiftx'])
121
123
    -> grid(-column=>1, -row=>9, -padx=>2);
122
 
  $widgets{atoms_shifty} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
124
  $widgets{atoms_shifty} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
123
125
                                        -validate=>'key',
124
126
                                        -validatecommand=>[\&set_atoms_params, 'shifty'])
125
127
    -> grid(-column=>1, -row=>10, -padx=>2);
126
 
  $widgets{atoms_shiftz} = $fr -> Entry(-width=>10, -font=>$config{gds}{font},
 
128
  $widgets{atoms_shiftz} = $fr -> Entry(-width=>10, -font=>$config{fonts}{fixed},
127
129
                                        -validate=>'key',
128
130
                                        -validatecommand=>[\&set_atoms_params, 'shiftz'])
129
131
    -> grid(-column=>1, -row=>11, -padx=>2);
137
139
                                  -header     => 1,
138
140
                                  -scrollbars => 'osoe',
139
141
                                  -background => $config{colors}{background},
140
 
                                  -font       => $config{gds}{font},
 
142
                                  -font       => $config{fonts}{fixed},
141
143
                                  -selectmode => 'extended',
142
144
                                  -selectbackground => $config{colors}{selected},
143
145
                                  -browsecmd  => \&atoms_edit,
151
153
                                                     -anchor=>'center',
152
154
                                                     -foreground=>$config{colors}{activehighlightcolor});
153
155
  $atoms_styles{normal}   = $atoms_list -> ItemStyle('text',
154
 
                                                     -font=>$config{gds}{font},
 
156
                                                     -font=>$config{fonts}{fixed},
155
157
                                                     -foreground=>$config{colors}{foreground},
156
158
                                                     -selectforeground=>$config{colors}{foreground},
157
159
                                                     -background=>$config{colors}{background});
158
160
  $atoms_styles{centered} = $atoms_list -> ItemStyle('text',
159
 
                                                     -font=>$config{gds}{font},
 
161
                                                     -font=>$config{fonts}{fixed},
160
162
                                                     -anchor=>'center',
161
163
                                                     -foreground=>$config{colors}{foreground},
162
164
                                                     -selectforeground=>$config{colors}{foreground},
192
194
  $atoms_list -> columnWidth(6, -char=>10);
193
195
 
194
196
  $atoms_styles{normal}   = $atoms_list -> ItemStyle('text',
195
 
                                                     -font=>$config{gds}{font},
 
197
                                                     -font=>$config{fonts}{fixed},
196
198
                                                     -foreground=>$config{colors}{foreground},
197
199
                                                     -selectforeground=>$config{colors}{foreground},
198
200
                                                     -background=>$config{colors}{background});
199
201
  $atoms_styles{centered} = $atoms_list -> ItemStyle('text',
200
 
                                                     -font=>$config{gds}{font},
 
202
                                                     -font=>$config{fonts}{fixed},
201
203
                                                     -anchor=>'center',
202
204
                                                     -foreground=>$config{colors}{foreground},
203
205
                                                     -selectforeground=>$config{colors}{foreground},
223
225
  #if ($config{atoms}{elem} eq 'menu') {
224
226
  #  my @elem_list;
225
227
  #  $widgets{atoms_elem} = $fr -> BrowseEntry(-label => "Element ",
 
228
#                                             -disabledforeground => $config{colors}{foreground},
 
229
#                                             -state => 'readonly',
226
230
#                                             -font=>$config{fonts}{small},
227
231
#                                             -foreground=>$config{colors}{activehighlightcolor},
228
232
#                                             -width=>5,
310
314
                   -title          => 'Artemis: Question...',
311
315
                   -buttons        => ['Import atoms.inp', 'Blank page', 'Cancel'],
312
316
                   -default_button => 'Blank page',
 
317
                   -font           => $config{fonts}{med},
313
318
                   -popover        => 'cursor');
314
319
  &posted_Dialog;
315
320
  my $answer = $dialog->Show();
536
541
                       -title          => 'Artemis: Question importing atoms.inp...',
537
542
                       -buttons        => ['Yes', 'No'],
538
543
                       -default_button => 'Yes',
 
544
                       -font           => $config{fonts}{med},
539
545
                       -popover        => 'cursor');
540
546
      &posted_Dialog;
541
547
      my $response = $dialog->Show();
954
960
  ## read titles and edge -- which is ok since the current must be
955
961
  ## showing, but also need to update them in case of clicking away
956
962
  ## and back before running
 
963
  atoms_new_site();
 
964
  $top->focus;
957
965
  atoms_save_page($current);
958
966
  Echo("Refreshed atoms parameters ...");
959
967
 
999
1007
  my $tag_bad = 0;
1000
1008
  my $xtal_warnings = q{};
1001
1009
  ##foreach my $k (sort (grep /^atoms_elem_\d+$/, (keys %widgets))) {
 
1010
  my $count = 0;
 
1011
  foreach my $s (@{ $paths{$current}->get("atoms_atoms") }) {
 
1012
    check_for_third($s, $count);
 
1013
    ++$count;
 
1014
  };
 
1015
  atoms_save_page($current);
1002
1016
  foreach my $s (@{ $paths{$current}->get("atoms_atoms") }) {
1003
1017
    $sites[$nsites] = Xray::Xtal::Site -> new($nsites);
1004
1018
    ## this mess allows for simple fractions and such
1034
1048
                     -title          => 'Artemis: Question...',
1035
1049
                     -buttons        => ['Yes, continue', 'No, cancel'],
1036
1050
                     -default_button => 'No, cancel',
 
1051
                     -font           => $config{fonts}{med},
1037
1052
                     -popover        => 'cursor');
1038
1053
    my $answer = $dialog->Show();
1039
1054
    if ($answer eq 'No, cancel') {
1159
1174
    #$widgets{feff_inptext} -> delete('1.0', 'end');
1160
1175
    #$widgets{feff_inptext} -> insert('1.0', $feff);
1161
1176
    $widgets{feff_inptext} -> Load(File::Spec->catfile($project_folder, $id, "feff.inp"));
 
1177
    $widgets{feff_inptext} -> tagAdd("feffinp", qw(1.0 end));
1162
1178
    $widgets{feff_inptext} -> ResetUndo;
1163
1179
    $fefftabs -> pageconfigure('feff.inp', -state=>'normal');
1164
1180
    $fefftabs -> raise('feff.inp');
1195
1211
  #print "$edge $absorber $z\n";
1196
1212
  return ($edge, $absorber, $is_odd);
1197
1213
};
 
1214
 
 
1215
sub check_for_third {
 
1216
  my ($site, $row) = @_;
 
1217
  my @col = (q{}, qw(x y z));
 
1218
  foreach my $coord (1, 2, 3) {
 
1219
    my $val = Xray::Atoms::number($site->[$coord], 1);  # watch out for fractions
 
1220
    my $diff = abs($val - THIRD);
 
1221
    my $id = $site->[4] || $site->[0];
 
1222
    if ( ($diff < DELTA) and ($diff > EPSILON) ) {
 
1223
      my $dialog =
 
1224
        $top -> Dialog(-bitmap         => 'questhead',
 
1225
                       -text           => "The $col[$coord] coordinate of $id is very close to 1/3.  Atoms and Feff operate at 5 digits of precision.  Do you want to use the value $site->[$coord] or should Artemis change this value to 1/3?",
 
1226
                       -title          => 'Artemis: Question...',
 
1227
                       -buttons        => ["Use $site->[$coord]", 'Change to 1/3'],
 
1228
                       -default_button => 'Change to 1/3',
 
1229
                       -font           => $config{fonts}{med},);
 
1230
      &posted_Dialog;
 
1231
      #$dialog->Subwidget("message")->configure(-width=>100);
 
1232
      my $answer = $dialog->Show();
 
1233
      if ($answer eq "Change to 1/3") {
 
1234
        $widgets{atoms_list} -> itemConfigure($row, $coord+2, -text=>"1/3");
 
1235
        $atoms[$row]->[$coord] = 0.33333;
 
1236
      };
 
1237
    };
 
1238
    $diff = abs($val - TWOTH);
 
1239
    if ( ($diff < DELTA) and ($diff > EPSILON) ) {
 
1240
      my $dialog =
 
1241
        $top -> Dialog(-bitmap         => 'questhead',
 
1242
                       -text           => "The $coord coordinate of $id is very close to 2/3.  Atoms and Feff operate at 5 digits of precision.  Do you want to use the value $site->[$coord] or should Artemis change this value to 2/3?",
 
1243
                       -title          => 'Artemis: Question...',
 
1244
                       -buttons        => ["Use $site->[$coord]", 'Change to 2/3'],
 
1245
                       -default_button => 'Change to 2/3',
 
1246
                       -font           => $config{fonts}{med},);
 
1247
      &posted_Dialog;
 
1248
      my $answer = $dialog->Show();
 
1249
      if ($answer eq "Change to 2/3") {
 
1250
        $widgets{atoms_list} -> itemConfigure($row, $coord+2, -text=>"2/3");
 
1251
        $atoms[$row]->[$coord] = 0.66667;
 
1252
      };
 
1253
    };
 
1254
  };
 
1255
};