root / ase / gui / gui.py @ 4
Historique | Voir | Annoter | Télécharger (41,34 ko)
| 1 | 1 | tkerber | # husk:
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|---|---|---|---|
| 2 | 1 | tkerber | # Exit*2? remove pylab.show()
|
| 3 | 1 | tkerber | # close button
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| 4 | 1 | tkerber | # DFT
|
| 5 | 1 | tkerber | # ADOS
|
| 6 | 1 | tkerber | # grey-out stuff after one second: vmd, rasmol, ...
|
| 7 | 1 | tkerber | # Show with ....
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| 8 | 1 | tkerber | # rasmol: set same rotation as ag
|
| 9 | 1 | tkerber | # Graphs: save, Python, 3D
|
| 10 | 1 | tkerber | # start from python (interactive mode?)
|
| 11 | 1 | tkerber | # ascii-art option (colored)|
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| 12 | 1 | tkerber | # option -o (output) and -f (force overwrite)
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| 13 | 1 | tkerber | # surfacebuilder
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| 14 | 1 | tkerber | # screen-dump
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| 15 | 1 | tkerber | # icon
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| 16 | 1 | tkerber | # ag-community-server
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| 17 | 1 | tkerber | # translate option: record all translations,
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| 18 | 1 | tkerber | # and check for missing translations.
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| 19 | 1 | tkerber | |
| 20 | 1 | tkerber | #TODO: Add possible way of choosing orinetations. \
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| 21 | 1 | tkerber | #TODO: Two atoms defines a direction, three atoms their normal does
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| 22 | 1 | tkerber | #TODO: Align orientations chosen in Rot_selected v unselcted
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| 23 | 1 | tkerber | #TODO: Get the atoms_rotate_0 thing string
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| 24 | 1 | tkerber | #TODO: Use set atoms instead og the get atoms
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| 25 | 1 | tkerber | #TODO: Arrow keys will decide how the orientation changes
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| 26 | 1 | tkerber | #TODO: Undo redo que should be implemented
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| 27 | 1 | tkerber | #TODO: Update should have possibility to change positions
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| 28 | 1 | tkerber | #TODO: Window for rotation modes and move moves which can be chosen
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| 29 | 1 | tkerber | #TODO: WHen rotate and move / hide the movie menu
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| 30 | 1 | tkerber | |
| 31 | 1 | tkerber | import os |
| 32 | 1 | tkerber | import weakref |
| 33 | 1 | tkerber | import numpy as np |
| 34 | 1 | tkerber | |
| 35 | 1 | tkerber | import gtk |
| 36 | 1 | tkerber | from ase.gui.view import View |
| 37 | 1 | tkerber | from ase.gui.status import Status |
| 38 | 1 | tkerber | from ase.gui.widgets import pack, help, Help, oops |
| 39 | 1 | tkerber | from ase.gui.languages import translate as _ |
| 40 | 1 | tkerber | |
| 41 | 1 | tkerber | from ase.gui.settings import Settings |
| 42 | 1 | tkerber | from ase.gui.surfaceslab import SetupSurfaceSlab |
| 43 | 1 | tkerber | from ase.gui.nanoparticle import SetupNanoparticle |
| 44 | 1 | tkerber | from ase.gui.nanotube import SetupNanotube |
| 45 | 1 | tkerber | from ase.gui.graphene import SetupGraphene |
| 46 | 1 | tkerber | from ase.gui.calculator import SetCalculator |
| 47 | 1 | tkerber | from ase.gui.energyforces import EnergyForces |
| 48 | 1 | tkerber | from ase.gui.minimize import Minimize |
| 49 | 1 | tkerber | from ase.gui.scaling import HomogeneousDeformation |
| 50 | 1 | tkerber | |
| 51 | 1 | tkerber | ui_info = """\
|
| 52 | 1 | tkerber | <ui>
|
| 53 | 1 | tkerber | <menubar name='MenuBar'>
|
| 54 | 1 | tkerber | <menu action='FileMenu'>
|
| 55 | 1 | tkerber | <menuitem action='Open'/>
|
| 56 | 1 | tkerber | <menuitem action='New'/>
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| 57 | 1 | tkerber | <menuitem action='Save'/>
|
| 58 | 1 | tkerber | <separator/>
|
| 59 | 1 | tkerber | <menuitem action='Quit'/>
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| 60 | 1 | tkerber | </menu>
|
| 61 | 1 | tkerber | <menu action='EditMenu'>
|
| 62 | 1 | tkerber | <menuitem action='SelectAll'/>
|
| 63 | 1 | tkerber | <menuitem action='Invert'/>
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| 64 | 1 | tkerber | <menuitem action='SelectConstrained'/>
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| 65 | 1 | tkerber | <separator/>
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| 66 | 1 | tkerber | <menuitem action='Modify'/>
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| 67 | 1 | tkerber | <menuitem action='AddAtoms'/>
|
| 68 | 1 | tkerber | <menuitem action='DeleteAtoms'/>
|
| 69 | 1 | tkerber | <separator/>
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| 70 | 1 | tkerber | <menuitem action='First'/>
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| 71 | 1 | tkerber | <menuitem action='Previous'/>
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| 72 | 1 | tkerber | <menuitem action='Next'/>
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| 73 | 1 | tkerber | <menuitem action='Last'/>
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| 74 | 1 | tkerber | </menu>
|
| 75 | 1 | tkerber | <menu action='ViewMenu'>
|
| 76 | 1 | tkerber | <menuitem action='ShowUnitCell'/>
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| 77 | 1 | tkerber | <menuitem action='ShowAxes'/>
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| 78 | 1 | tkerber | <menuitem action='ShowBonds'/>
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| 79 | 1 | tkerber | <separator/>
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| 80 | 1 | tkerber | <menuitem action='Repeat'/>
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| 81 | 1 | tkerber | <menuitem action='Rotate'/>
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| 82 | 1 | tkerber | <menuitem action='Focus'/>
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| 83 | 1 | tkerber | <menuitem action='ZoomIn'/>
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| 84 | 1 | tkerber | <menuitem action='ZoomOut'/>
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| 85 | 1 | tkerber | <menuitem action='Settings'/>
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| 86 | 1 | tkerber | <menuitem action='VMD'/>
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| 87 | 1 | tkerber | <menuitem action='RasMol'/>
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| 88 | 1 | tkerber | <menuitem action='XMakeMol'/>
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| 89 | 1 | tkerber | <menuitem action='Avogadro'/>
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| 90 | 1 | tkerber | </menu>
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| 91 | 1 | tkerber | <menu action='ToolsMenu'>
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| 92 | 1 | tkerber | <menuitem action='Graphs'/>
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| 93 | 1 | tkerber | <menuitem action='Movie'/>
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| 94 | 1 | tkerber | <menuitem action='EModify'/>
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| 95 | 1 | tkerber | <menuitem action='Constraints'/>
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| 96 | 1 | tkerber | <menuitem action='MoveAtoms'/>
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| 97 | 1 | tkerber | <menuitem action='RotateAtoms'/>
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| 98 | 1 | tkerber | <menuitem action='OrientAtoms'/>
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| 99 | 1 | tkerber | <menuitem action='DFT'/>
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| 100 | 1 | tkerber | <menuitem action='NEB'/>
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| 101 | 1 | tkerber | <menuitem action='BulkModulus'/>
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| 102 | 1 | tkerber | </menu>
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| 103 | 1 | tkerber | <menu action='SetupMenu'>
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| 104 | 1 | tkerber | <menuitem action='Surface'/>
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| 105 | 1 | tkerber | <menuitem action='Nanoparticle'/>
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| 106 | 1 | tkerber | <menuitem action='Graphene'/>
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| 107 | 1 | tkerber | <menuitem action='Nanotube'/>
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| 108 | 1 | tkerber | </menu>
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| 109 | 1 | tkerber | <menu action='CalculateMenu'>
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| 110 | 1 | tkerber | <menuitem action='SetCalculator'/>
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| 111 | 1 | tkerber | <separator/>
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| 112 | 1 | tkerber | <menuitem action='EnergyForces'/>
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| 113 | 1 | tkerber | <menuitem action='Minimize'/>
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| 114 | 1 | tkerber | <menuitem action='Scaling'/>
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| 115 | 1 | tkerber | </menu>
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| 116 | 1 | tkerber | <menu action='HelpMenu'>
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| 117 | 1 | tkerber | <menuitem action='About'/>
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| 118 | 1 | tkerber | <menuitem action='Webpage'/>
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| 119 | 1 | tkerber | <menuitem action='Debug'/>
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| 120 | 1 | tkerber | </menu>
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| 121 | 1 | tkerber | </menubar>
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| 122 | 1 | tkerber | </ui>"""
|
| 123 | 1 | tkerber | |
| 124 | 1 | tkerber | class GUI(View, Status): |
| 125 | 1 | tkerber | def __init__(self, images, rotations='', show_unit_cell=True, |
| 126 | 1 | tkerber | show_bonds=False):
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| 127 | 1 | tkerber | self.images = images
|
| 128 | 1 | tkerber | self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
|
| 129 | 1 | tkerber | #self.window.set_icon(gtk.gdk.pixbuf_new_from_file('guiase.png'))
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| 130 | 1 | tkerber | self.window.set_position(gtk.WIN_POS_CENTER)
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| 131 | 1 | tkerber | #self.window.connect("destroy", lambda w: gtk.main_quit())
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| 132 | 1 | tkerber | self.window.connect('delete_event', self.exit) |
| 133 | 1 | tkerber | vbox = gtk.VBox() |
| 134 | 1 | tkerber | self.window.add(vbox)
|
| 135 | 1 | tkerber | if gtk.pygtk_version < (2, 12): |
| 136 | 1 | tkerber | self.set_tip = gtk.Tooltips().set_tip
|
| 137 | 1 | tkerber | |
| 138 | 1 | tkerber | actions = gtk.ActionGroup("Actions")
|
| 139 | 1 | tkerber | actions.add_actions([ |
| 140 | 1 | tkerber | ('FileMenu', None, '_File'), |
| 141 | 1 | tkerber | ('EditMenu', None, '_Edit'), |
| 142 | 1 | tkerber | ('ViewMenu', None, '_View' ), |
| 143 | 1 | tkerber | ('ToolsMenu', None, '_Tools'), |
| 144 | 1 | tkerber | ('SetupMenu', None, '_Setup'), |
| 145 | 1 | tkerber | ('CalculateMenu', None, '_Calculate'), |
| 146 | 1 | tkerber | ('HelpMenu', None, '_Help'), |
| 147 | 1 | tkerber | ('Open', gtk.STOCK_OPEN, '_Open', '<control>O', |
| 148 | 1 | tkerber | 'Create a new file',
|
| 149 | 1 | tkerber | self.open),
|
| 150 | 1 | tkerber | ('New', gtk.STOCK_NEW, '_New', '<control>N', |
| 151 | 1 | tkerber | 'New ase.gui window',
|
| 152 | 1 | tkerber | lambda widget: os.system('ag &')), |
| 153 | 1 | tkerber | ('Save', gtk.STOCK_SAVE, '_Save', '<control>S', |
| 154 | 1 | tkerber | 'Save current file',
|
| 155 | 1 | tkerber | self.save),
|
| 156 | 1 | tkerber | ('Quit', gtk.STOCK_QUIT, '_Quit', '<control>Q', |
| 157 | 1 | tkerber | 'Quit',
|
| 158 | 1 | tkerber | self.exit),
|
| 159 | 1 | tkerber | ('SelectAll', None, 'Select _all', None, |
| 160 | 1 | tkerber | '',
|
| 161 | 1 | tkerber | self.select_all),
|
| 162 | 1 | tkerber | ('Invert', None, '_Invert selection', None, |
| 163 | 1 | tkerber | '',
|
| 164 | 1 | tkerber | self.invert_selection),
|
| 165 | 1 | tkerber | ('SelectConstrained', None, 'Select _constrained atoms', None, |
| 166 | 1 | tkerber | '',
|
| 167 | 1 | tkerber | self.select_constrained_atoms),
|
| 168 | 1 | tkerber | ('Modify', None, '_Modify', '<control>Y', |
| 169 | 1 | tkerber | 'Change tags, moments and atom types of the selected atoms',
|
| 170 | 1 | tkerber | self.modify_atoms),
|
| 171 | 1 | tkerber | ('AddAtoms', None, '_Add atoms', '<control>A', |
| 172 | 1 | tkerber | 'Insert or import atoms and molecules',
|
| 173 | 1 | tkerber | self.add_atoms),
|
| 174 | 1 | tkerber | ('DeleteAtoms', None, '_Delete selected atoms', 'BackSpace', |
| 175 | 1 | tkerber | 'Deletes the selected atoms',
|
| 176 | 1 | tkerber | self.delete_selected_atoms),
|
| 177 | 1 | tkerber | ('First', gtk.STOCK_GOTO_FIRST, '_First image', 'Home', |
| 178 | 1 | tkerber | '',
|
| 179 | 1 | tkerber | self.step),
|
| 180 | 1 | tkerber | ('Previous', gtk.STOCK_GO_BACK, '_Previous image', 'Page_Up', |
| 181 | 1 | tkerber | '',
|
| 182 | 1 | tkerber | self.step),
|
| 183 | 1 | tkerber | ('Next', gtk.STOCK_GO_FORWARD, '_Next image', 'Page_Down', |
| 184 | 1 | tkerber | '',
|
| 185 | 1 | tkerber | self.step),
|
| 186 | 1 | tkerber | ('Last', gtk.STOCK_GOTO_LAST, '_Last image', 'End', |
| 187 | 1 | tkerber | '',
|
| 188 | 1 | tkerber | self.step),
|
| 189 | 1 | tkerber | ('Repeat', None, 'Repeat ...', None, |
| 190 | 1 | tkerber | '',
|
| 191 | 1 | tkerber | self.repeat_window),
|
| 192 | 1 | tkerber | ('Rotate', None, 'Rotate ...', None, |
| 193 | 1 | tkerber | '',
|
| 194 | 1 | tkerber | self.rotate_window),
|
| 195 | 1 | tkerber | ('Focus', gtk.STOCK_ZOOM_FIT, 'Focus', 'F', |
| 196 | 1 | tkerber | '',
|
| 197 | 1 | tkerber | self.focus),
|
| 198 | 1 | tkerber | ('ZoomIn', gtk.STOCK_ZOOM_IN, 'Zoom in', 'plus', |
| 199 | 1 | tkerber | '',
|
| 200 | 1 | tkerber | self.zoom),
|
| 201 | 1 | tkerber | ('ZoomOut', gtk.STOCK_ZOOM_OUT, 'Zoom out', 'minus', |
| 202 | 1 | tkerber | '',
|
| 203 | 1 | tkerber | self.zoom),
|
| 204 | 1 | tkerber | ('Settings', gtk.STOCK_PREFERENCES, 'Settings ...', None, |
| 205 | 1 | tkerber | '',
|
| 206 | 1 | tkerber | self.settings),
|
| 207 | 1 | tkerber | ('VMD', None, 'VMD', None, |
| 208 | 1 | tkerber | '',
|
| 209 | 1 | tkerber | self.external_viewer),
|
| 210 | 1 | tkerber | ('RasMol', None, 'RasMol', None, |
| 211 | 1 | tkerber | '',
|
| 212 | 1 | tkerber | self.external_viewer),
|
| 213 | 1 | tkerber | ('XMakeMol', None, 'xmakemol', None, |
| 214 | 1 | tkerber | '',
|
| 215 | 1 | tkerber | self.external_viewer),
|
| 216 | 1 | tkerber | ('Avogadro', None, 'avogadro', None, |
| 217 | 1 | tkerber | '',
|
| 218 | 1 | tkerber | self.external_viewer),
|
| 219 | 1 | tkerber | ('Graphs', None, 'Graphs ...', None, |
| 220 | 1 | tkerber | '',
|
| 221 | 1 | tkerber | self.plot_graphs),
|
| 222 | 1 | tkerber | ('Movie', None, 'Movie ...', None, |
| 223 | 1 | tkerber | '',
|
| 224 | 1 | tkerber | self.movie),
|
| 225 | 1 | tkerber | ('EModify', None, 'Expert modify ...', None, |
| 226 | 1 | tkerber | '',
|
| 227 | 1 | tkerber | self.execute),
|
| 228 | 1 | tkerber | ('Constraints', None, 'Constraints ...', None, |
| 229 | 1 | tkerber | '',
|
| 230 | 1 | tkerber | self.constraints_window),
|
| 231 | 1 | tkerber | ('DFT', None, 'DFT ...', None, |
| 232 | 1 | tkerber | '',
|
| 233 | 1 | tkerber | self.dft_window),
|
| 234 | 1 | tkerber | ('NEB', None, 'NE_B', None, |
| 235 | 1 | tkerber | '',
|
| 236 | 1 | tkerber | self.NEB),
|
| 237 | 1 | tkerber | ('BulkModulus', None, 'B_ulk Modulus', None, |
| 238 | 1 | tkerber | '',
|
| 239 | 1 | tkerber | self.bulk_modulus),
|
| 240 | 1 | tkerber | ('Bulk', None, '_Bulk Crystal', None, |
| 241 | 1 | tkerber | "Create a bulk crystal with arbitrary orientation",
|
| 242 | 1 | tkerber | self.bulk_window),
|
| 243 | 1 | tkerber | ('Surface', None, '_Surface slab', None, |
| 244 | 1 | tkerber | "Create the most common surfaces",
|
| 245 | 1 | tkerber | self.surface_window),
|
| 246 | 1 | tkerber | ('Nanoparticle', None, '_Nanoparticle', None, |
| 247 | 1 | tkerber | "Create a crystalline nanoparticle",
|
| 248 | 1 | tkerber | self.nanoparticle_window),
|
| 249 | 1 | tkerber | ('Nanotube', None, 'Nano_tube', None, |
| 250 | 1 | tkerber | "Create a nanotube",
|
| 251 | 1 | tkerber | self.nanotube_window),
|
| 252 | 1 | tkerber | ('Graphene', None, 'Graphene', None, |
| 253 | 1 | tkerber | "Create a graphene sheet or nanoribbon",
|
| 254 | 1 | tkerber | self.graphene_window),
|
| 255 | 1 | tkerber | ('SetCalculator', None, 'Set _Calculator', None, |
| 256 | 1 | tkerber | "Set a calculator used in all calculation modules",
|
| 257 | 1 | tkerber | self.calculator_window),
|
| 258 | 1 | tkerber | ('EnergyForces', None, '_Energy and Forces', None, |
| 259 | 1 | tkerber | "Calculate energy and forces",
|
| 260 | 1 | tkerber | self.energy_window),
|
| 261 | 1 | tkerber | ('Minimize', None, 'Energy _Minimization', None, |
| 262 | 1 | tkerber | "Minimize the energy",
|
| 263 | 1 | tkerber | self.energy_minimize_window),
|
| 264 | 1 | tkerber | ('Scaling', None, 'Scale system', None, |
| 265 | 1 | tkerber | "Deform system by scaling it",
|
| 266 | 1 | tkerber | self.scaling_window),
|
| 267 | 1 | tkerber | ('About', None, '_About', None, |
| 268 | 1 | tkerber | None,
|
| 269 | 1 | tkerber | self.about),
|
| 270 | 1 | tkerber | ('Webpage', gtk.STOCK_HELP, 'Webpage ...', None, None, webpage), |
| 271 | 1 | tkerber | ('Debug', None, 'Debug ...', None, None, self.debug)]) |
| 272 | 1 | tkerber | actions.add_toggle_actions([ |
| 273 | 1 | tkerber | ('ShowUnitCell', None, 'Show _unit cell', '<control>U', |
| 274 | 1 | tkerber | 'Bold',
|
| 275 | 1 | tkerber | self.toggle_show_unit_cell,
|
| 276 | 1 | tkerber | show_unit_cell > 0),
|
| 277 | 1 | tkerber | ('ShowAxes', None, 'Show _axes', None, |
| 278 | 1 | tkerber | 'Bold',
|
| 279 | 1 | tkerber | self.toggle_show_axes,
|
| 280 | 1 | tkerber | True),
|
| 281 | 1 | tkerber | ('ShowBonds', None, 'Show _bonds', '<control>B', |
| 282 | 1 | tkerber | 'Bold',
|
| 283 | 1 | tkerber | self.toggle_show_bonds,
|
| 284 | 1 | tkerber | show_bonds), |
| 285 | 1 | tkerber | ('MoveAtoms', None, '_Move atoms', '<control>M', |
| 286 | 1 | tkerber | 'Bold',
|
| 287 | 1 | tkerber | self.toggle_move_mode,
|
| 288 | 1 | tkerber | False),
|
| 289 | 1 | tkerber | ('RotateAtoms', None, '_Rotate atoms', '<control>R', |
| 290 | 1 | tkerber | 'Bold',
|
| 291 | 1 | tkerber | self.toggle_rotate_mode,
|
| 292 | 1 | tkerber | False),
|
| 293 | 1 | tkerber | ('OrientAtoms', None, 'Orien_t atoms', '<control>T', |
| 294 | 1 | tkerber | 'Bold',
|
| 295 | 1 | tkerber | self.toggle_orient_mode,
|
| 296 | 1 | tkerber | False)
|
| 297 | 1 | tkerber | ]) |
| 298 | 1 | tkerber | self.ui = ui = gtk.UIManager()
|
| 299 | 1 | tkerber | ui.insert_action_group(actions, 0)
|
| 300 | 1 | tkerber | self.window.add_accel_group(ui.get_accel_group())
|
| 301 | 1 | tkerber | |
| 302 | 1 | tkerber | try:
|
| 303 | 1 | tkerber | mergeid = ui.add_ui_from_string(ui_info) |
| 304 | 1 | tkerber | except gobject.GError, msg:
|
| 305 | 1 | tkerber | print 'building menus failed: %s' % msg |
| 306 | 1 | tkerber | |
| 307 | 1 | tkerber | vbox.pack_start(ui.get_widget('/MenuBar'), False, False, 0) |
| 308 | 1 | tkerber | |
| 309 | 1 | tkerber | View.__init__(self, vbox, rotations)
|
| 310 | 1 | tkerber | Status.__init__(self, vbox)
|
| 311 | 1 | tkerber | vbox.show() |
| 312 | 1 | tkerber | #self.window.set_events(gtk.gdk.BUTTON_PRESS_MASK)
|
| 313 | 1 | tkerber | self.window.connect('key-press-event', self.scroll) |
| 314 | 1 | tkerber | self.window.connect('scroll_event', self.scroll_event) |
| 315 | 1 | tkerber | self.window.show()
|
| 316 | 1 | tkerber | self.graphs = [] # List of open pylab windows |
| 317 | 1 | tkerber | self.graph_wref = [] # List of weakrefs to Graph objects |
| 318 | 1 | tkerber | self.movie_window = None |
| 319 | 1 | tkerber | self.vulnerable_windows = []
|
| 320 | 1 | tkerber | self.simulation = {} # Used by modules on Calculate menu. |
| 321 | 1 | tkerber | self.module_state = {} # Used by modules to store their state. |
| 322 | 1 | tkerber | |
| 323 | 1 | tkerber | def run(self, expr=None): |
| 324 | 1 | tkerber | self.set_colors()
|
| 325 | 1 | tkerber | self.set_coordinates(self.images.nimages - 1, focus=True) |
| 326 | 1 | tkerber | |
| 327 | 1 | tkerber | if self.images.nimages > 1: |
| 328 | 1 | tkerber | self.movie()
|
| 329 | 1 | tkerber | |
| 330 | 1 | tkerber | if expr is None and not np.isnan(self.images.E[0]): |
| 331 | 1 | tkerber | expr = 'i, e - E[-1]'
|
| 332 | 1 | tkerber | |
| 333 | 1 | tkerber | if expr is not None and expr != '' and self.images.nimages > 1: |
| 334 | 1 | tkerber | self.plot_graphs(expr=expr)
|
| 335 | 1 | tkerber | |
| 336 | 1 | tkerber | gtk.main() |
| 337 | 1 | tkerber | |
| 338 | 1 | tkerber | |
| 339 | 1 | tkerber | def step(self, action): |
| 340 | 1 | tkerber | d = {'First': -10000000,
|
| 341 | 1 | tkerber | 'Previous': -1, |
| 342 | 1 | tkerber | 'Next': 1, |
| 343 | 1 | tkerber | 'Last': 10000000}[action.get_name()] |
| 344 | 1 | tkerber | i = max(0, min(self.images.nimages - 1, self.frame + d)) |
| 345 | 1 | tkerber | self.set_frame(i)
|
| 346 | 1 | tkerber | if self.movie_window is not None: |
| 347 | 1 | tkerber | self.movie_window.frame_number.value = i
|
| 348 | 1 | tkerber | |
| 349 | 1 | tkerber | def _do_zoom(self, x): |
| 350 | 1 | tkerber | """Utility method for zooming"""
|
| 351 | 1 | tkerber | self.scale *= x
|
| 352 | 1 | tkerber | self.draw()
|
| 353 | 1 | tkerber | |
| 354 | 1 | tkerber | def zoom(self, action): |
| 355 | 1 | tkerber | """Zoom in/out on keypress or clicking menu item"""
|
| 356 | 1 | tkerber | x = {'ZoomIn': 1.2, 'ZoomOut':1 / 1.2}[action.get_name()]
|
| 357 | 1 | tkerber | self._do_zoom(x)
|
| 358 | 1 | tkerber | |
| 359 | 1 | tkerber | def scroll_event(self, window, event): |
| 360 | 1 | tkerber | """Zoom in/out when using mouse wheel"""
|
| 361 | 1 | tkerber | x = 1.0
|
| 362 | 1 | tkerber | if event.direction == gtk.gdk.SCROLL_UP:
|
| 363 | 1 | tkerber | x = 1.2
|
| 364 | 1 | tkerber | elif event.direction == gtk.gdk.SCROLL_DOWN:
|
| 365 | 1 | tkerber | x = 1.0 / 1.2 |
| 366 | 1 | tkerber | self._do_zoom(x)
|
| 367 | 1 | tkerber | |
| 368 | 1 | tkerber | def settings(self, menuitem): |
| 369 | 1 | tkerber | Settings(self)
|
| 370 | 1 | tkerber | |
| 371 | 1 | tkerber | def scroll(self, window, event): |
| 372 | 1 | tkerber | from copy import copy |
| 373 | 1 | tkerber | CTRL = event.state == gtk.gdk.CONTROL_MASK |
| 374 | 1 | tkerber | SHIFT = event.state == gtk.gdk.SHIFT_MASK |
| 375 | 1 | tkerber | dxdydz = {gtk.keysyms.KP_Add: ('zoom', 1.2, 0),
|
| 376 | 1 | tkerber | gtk.keysyms.KP_Subtract: ('zoom', 1 / 1.2, 0), |
| 377 | 1 | tkerber | gtk.keysyms.Up: ( 0, +1 - CTRL, +CTRL), |
| 378 | 1 | tkerber | gtk.keysyms.Down: ( 0, -1 + CTRL, -CTRL), |
| 379 | 1 | tkerber | gtk.keysyms.Right: (+1, 0, 0), |
| 380 | 1 | tkerber | gtk.keysyms.Left: (-1, 0, 0)}.get(event.keyval, None) |
| 381 | 1 | tkerber | try:
|
| 382 | 1 | tkerber | inch = chr(event.keyval)
|
| 383 | 1 | tkerber | except:
|
| 384 | 1 | tkerber | inch = None
|
| 385 | 1 | tkerber | |
| 386 | 1 | tkerber | sel = [] |
| 387 | 1 | tkerber | |
| 388 | 1 | tkerber | atom_move = self.ui.get_widget('/MenuBar/ToolsMenu/MoveAtoms' |
| 389 | 1 | tkerber | ).get_active() |
| 390 | 1 | tkerber | atom_rotate = self.ui.get_widget('/MenuBar/ToolsMenu/RotateAtoms' |
| 391 | 1 | tkerber | ).get_active() |
| 392 | 1 | tkerber | atom_orient = self.ui.get_widget('/MenuBar/ToolsMenu/OrientAtoms' |
| 393 | 1 | tkerber | ).get_active() |
| 394 | 1 | tkerber | if dxdydz is None: |
| 395 | 1 | tkerber | return
|
| 396 | 1 | tkerber | dx, dy, dz = dxdydz |
| 397 | 1 | tkerber | if dx == 'zoom': |
| 398 | 1 | tkerber | self._do_zoom(dy)
|
| 399 | 1 | tkerber | return
|
| 400 | 1 | tkerber | if dx == 'zoom': |
| 401 | 1 | tkerber | self._do_zoom(dy)
|
| 402 | 1 | tkerber | return
|
| 403 | 1 | tkerber | d = self.scale * 0.1 |
| 404 | 1 | tkerber | tvec = np.array([dx, dy, dz]) |
| 405 | 1 | tkerber | |
| 406 | 1 | tkerber | dir_vec = np.dot(self.axes, tvec)
|
| 407 | 1 | tkerber | if (atom_move):
|
| 408 | 1 | tkerber | rotmat = self.axes
|
| 409 | 1 | tkerber | s = 0.1
|
| 410 | 1 | tkerber | if SHIFT:
|
| 411 | 1 | tkerber | s = 0.01
|
| 412 | 1 | tkerber | add = s * dir_vec |
| 413 | 1 | tkerber | for i in range(len(self.R)): |
| 414 | 1 | tkerber | if self.atoms_to_rotate_0[i]: |
| 415 | 1 | tkerber | self.R[i] += add
|
| 416 | 1 | tkerber | for jx in range(self.images.nimages): |
| 417 | 1 | tkerber | self.images.P[jx][i] += add
|
| 418 | 1 | tkerber | elif atom_rotate:
|
| 419 | 1 | tkerber | from rot_tools import rotate_about_vec, \ |
| 420 | 1 | tkerber | rotate_vec
|
| 421 | 1 | tkerber | sel = self.images.selected
|
| 422 | 1 | tkerber | if sum(sel) == 0: |
| 423 | 1 | tkerber | sel = self.atoms_to_rotate_0
|
| 424 | 1 | tkerber | nsel = sum(sel)
|
| 425 | 1 | tkerber | # this is the first one to get instatiated
|
| 426 | 1 | tkerber | if nsel != 2: |
| 427 | 1 | tkerber | self.rot_vec = dir_vec
|
| 428 | 1 | tkerber | |
| 429 | 1 | tkerber | change = False
|
| 430 | 1 | tkerber | z_axis = np.dot(self.axes, np.array([0, 0, 1])) |
| 431 | 1 | tkerber | if self.atoms_to_rotate == None: |
| 432 | 1 | tkerber | change = True
|
| 433 | 1 | tkerber | self.z_axis_old = z_axis.copy()
|
| 434 | 1 | tkerber | self.dx_change = [0, 0] |
| 435 | 1 | tkerber | self.atoms_to_rotate = self.atoms_to_rotate_0.copy() |
| 436 | 1 | tkerber | self.atoms_selected = sel.copy()
|
| 437 | 1 | tkerber | self.rot_vec = dir_vec
|
| 438 | 1 | tkerber | |
| 439 | 1 | tkerber | if nsel != 2 or sum(self.atoms_to_rotate) == 2: |
| 440 | 1 | tkerber | self.dx_change = [0, 0] |
| 441 | 1 | tkerber | |
| 442 | 1 | tkerber | for i in range(len(sel)): |
| 443 | 1 | tkerber | if sel[i] != self.atoms_selected[i]: |
| 444 | 1 | tkerber | change = True
|
| 445 | 1 | tkerber | cz = [dx, dy+dz] |
| 446 | 1 | tkerber | |
| 447 | 1 | tkerber | if cz[0] or cz[1]: |
| 448 | 1 | tkerber | change = False
|
| 449 | 1 | tkerber | if not(cz[0] * (self.dx_change[1])): |
| 450 | 1 | tkerber | change = True
|
| 451 | 1 | tkerber | for i in range(2): |
| 452 | 1 | tkerber | if cz[i] and self.dx_change[i]: |
| 453 | 1 | tkerber | self.rot_vec = self.rot_vec * cz[i] * self.dx_change[i] |
| 454 | 1 | tkerber | if cz[1]: |
| 455 | 1 | tkerber | change = False
|
| 456 | 1 | tkerber | |
| 457 | 1 | tkerber | if np.prod(self.z_axis_old != z_axis): |
| 458 | 1 | tkerber | change = True
|
| 459 | 1 | tkerber | self.z_axis_old = z_axis.copy()
|
| 460 | 1 | tkerber | self.dx_change = copy(cz)
|
| 461 | 1 | tkerber | dihedral_rotation = len(self.images.selected_ordered) == 4 |
| 462 | 1 | tkerber | |
| 463 | 1 | tkerber | if change:
|
| 464 | 1 | tkerber | self.atoms_selected = sel.copy()
|
| 465 | 1 | tkerber | |
| 466 | 1 | tkerber | if nsel == 2 and sum(self.atoms_to_rotate) != 2: |
| 467 | 1 | tkerber | asel = [] |
| 468 | 1 | tkerber | for i, j in enumerate(sel): |
| 469 | 1 | tkerber | if j:
|
| 470 | 1 | tkerber | asel.append(i) |
| 471 | 1 | tkerber | a1, a2 = asel |
| 472 | 1 | tkerber | |
| 473 | 1 | tkerber | rvx = self.images.P[self.frame][a1] - \ |
| 474 | 1 | tkerber | self.images.P[self.frame][a2] |
| 475 | 1 | tkerber | |
| 476 | 1 | tkerber | rvy = np.cross(rvx, |
| 477 | 1 | tkerber | np.dot(self.axes,
|
| 478 | 1 | tkerber | np.array([0, 0, 1]))) |
| 479 | 1 | tkerber | self.rot_vec = rvx * dx + rvy * (dy + dz)
|
| 480 | 1 | tkerber | self.dx_change = [dx, dy+dz]
|
| 481 | 1 | tkerber | |
| 482 | 1 | tkerber | # dihedral rotation?
|
| 483 | 1 | tkerber | if dihedral_rotation:
|
| 484 | 1 | tkerber | sel = self.images.selected_ordered
|
| 485 | 1 | tkerber | self.rot_vec = (dx+dy+dz)*(self.R[sel[2]]-self.R[sel[1]]) |
| 486 | 1 | tkerber | |
| 487 | 1 | tkerber | rot_cen = np.array([0.0, 0.0, 0.0]) |
| 488 | 1 | tkerber | if dihedral_rotation:
|
| 489 | 1 | tkerber | sel = self.images.selected_ordered
|
| 490 | 1 | tkerber | rot_cen = self.R[sel[1]].copy() |
| 491 | 1 | tkerber | elif nsel:
|
| 492 | 1 | tkerber | for i, b in enumerate( sel): |
| 493 | 1 | tkerber | if b:
|
| 494 | 1 | tkerber | rot_cen += self.R[i]
|
| 495 | 1 | tkerber | rot_cen /= float(nsel)
|
| 496 | 1 | tkerber | |
| 497 | 1 | tkerber | degrees = 5 * (1 - SHIFT) + SHIFT |
| 498 | 1 | tkerber | degrees = abs(sum(dxdydz)) * 3.1415 / 360.0 * degrees |
| 499 | 1 | tkerber | rotmat = rotate_about_vec(self.rot_vec, degrees)
|
| 500 | 1 | tkerber | |
| 501 | 1 | tkerber | # now rotate the atoms that are to be rotated
|
| 502 | 1 | tkerber | for i in range(len(self.R)): |
| 503 | 1 | tkerber | if self.atoms_to_rotate[i]: |
| 504 | 1 | tkerber | self.R[i] -= rot_cen
|
| 505 | 1 | tkerber | for jx in range(self.images.nimages): |
| 506 | 1 | tkerber | self.images.P[jx][i] -= rot_cen
|
| 507 | 1 | tkerber | |
| 508 | 1 | tkerber | self.R[i] = rotate_vec(rotmat, self.R[i]) |
| 509 | 1 | tkerber | for jx in range(self.images.nimages): |
| 510 | 1 | tkerber | self.images.P[jx][i] = rotate_vec(rotmat, self.images.P[jx][i]) |
| 511 | 1 | tkerber | |
| 512 | 1 | tkerber | self.R[i] += rot_cen
|
| 513 | 1 | tkerber | for jx in range(self.images.nimages): |
| 514 | 1 | tkerber | self.images.P[jx][i] += rot_cen
|
| 515 | 1 | tkerber | elif atom_orient:
|
| 516 | 1 | tkerber | to_vec = np.array([dx, dy, dz]) |
| 517 | 1 | tkerber | |
| 518 | 1 | tkerber | from rot_tools import rotate_vec_into_newvec |
| 519 | 1 | tkerber | rot_mat = rotate_vec_into_newvec(self.orient_normal, to_vec)
|
| 520 | 1 | tkerber | self.axes = rot_mat
|
| 521 | 1 | tkerber | |
| 522 | 1 | tkerber | self.set_coordinates()
|
| 523 | 1 | tkerber | else:
|
| 524 | 1 | tkerber | self.center -= (dx * 0.1 * self.axes[:, 0] - |
| 525 | 1 | tkerber | dy * 0.1 * self.axes[:, 1]) |
| 526 | 1 | tkerber | self.draw()
|
| 527 | 1 | tkerber | |
| 528 | 1 | tkerber | |
| 529 | 1 | tkerber | def add_atoms(self, widget, data=None): |
| 530 | 1 | tkerber | """
|
| 531 | 1 | tkerber | Presents a dialogbox to the user, that allows him to add atoms/molecule to the current slab.
|
| 532 | 1 | tkerber |
|
| 533 | 1 | tkerber | The molecule/atom is rotated using the current rotation of the coordinate system.
|
| 534 | 1 | tkerber |
|
| 535 | 1 | tkerber | The molecule/atom can be added at a specified position - if the keyword auto+Z is used,
|
| 536 | 1 | tkerber | the COM of the selected atoms will be used as COM for the moleculed. The COM is furthermore
|
| 537 | 1 | tkerber | translated Z ang towards the user.
|
| 538 | 1 | tkerber |
|
| 539 | 1 | tkerber | If no molecules are selected, the COM of all the atoms will be used for the x-y components of the
|
| 540 | 1 | tkerber | active coordinate system, while the z-direction will be chosen from the nearest atom position
|
| 541 | 1 | tkerber | along this direction.
|
| 542 | 1 | tkerber |
|
| 543 | 1 | tkerber | Note: If this option is used, all frames except the active one are deleted.
|
| 544 | 1 | tkerber | """
|
| 545 | 1 | tkerber | if data:
|
| 546 | 1 | tkerber | if data == 'load': |
| 547 | 1 | tkerber | chooser = gtk.FileChooserDialog( |
| 548 | 1 | tkerber | _('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 549 | 1 | tkerber | (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 550 | 1 | tkerber | gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 551 | 1 | tkerber | ok = chooser.run() |
| 552 | 1 | tkerber | if ok == gtk.RESPONSE_OK:
|
| 553 | 1 | tkerber | filename = chooser.get_filename() |
| 554 | 1 | tkerber | chooser.destroy() |
| 555 | 1 | tkerber | if not ok: |
| 556 | 1 | tkerber | return
|
| 557 | 1 | tkerber | |
| 558 | 1 | tkerber | if data == 'OK' or data == 'load': |
| 559 | 1 | tkerber | import ase |
| 560 | 1 | tkerber | if data == 'load': |
| 561 | 1 | tkerber | molecule = filename |
| 562 | 1 | tkerber | else:
|
| 563 | 1 | tkerber | molecule = self.add_entries[1].get_text() |
| 564 | 1 | tkerber | tag = self.add_entries[2].get_text() |
| 565 | 1 | tkerber | mom = self.add_entries[3].get_text() |
| 566 | 1 | tkerber | pos = self.add_entries[4].get_text().lower() |
| 567 | 1 | tkerber | |
| 568 | 1 | tkerber | a = None
|
| 569 | 1 | tkerber | try:
|
| 570 | 1 | tkerber | a = ase.Atoms([ase.Atom(molecule)]) |
| 571 | 1 | tkerber | except:
|
| 572 | 1 | tkerber | try:
|
| 573 | 1 | tkerber | a = ase.molecule(molecule) |
| 574 | 1 | tkerber | except:
|
| 575 | 1 | tkerber | try:
|
| 576 | 1 | tkerber | a = ase.read(molecule, -1)
|
| 577 | 1 | tkerber | except:
|
| 578 | 1 | tkerber | self.add_entries[1].set_text('?' + molecule) |
| 579 | 1 | tkerber | return ()
|
| 580 | 1 | tkerber | |
| 581 | 1 | tkerber | directions = np.transpose(self.axes)
|
| 582 | 1 | tkerber | if a != None: |
| 583 | 1 | tkerber | for i in a: |
| 584 | 1 | tkerber | try:
|
| 585 | 1 | tkerber | i.set_tag(int(tag))
|
| 586 | 1 | tkerber | except:
|
| 587 | 1 | tkerber | self.add_entries[2].set_text('?' + tag) |
| 588 | 1 | tkerber | return ()
|
| 589 | 1 | tkerber | try:
|
| 590 | 1 | tkerber | i.magmom = float(mom)
|
| 591 | 1 | tkerber | except:
|
| 592 | 1 | tkerber | self.add_entries[3].set_text('?' + mom) |
| 593 | 1 | tkerber | return ()
|
| 594 | 1 | tkerber | # apply the current rotation matrix to A
|
| 595 | 1 | tkerber | for i in a: |
| 596 | 1 | tkerber | i.position = np.dot(self.axes, i.position)
|
| 597 | 1 | tkerber | # find the extent of the molecule in the local coordinate system
|
| 598 | 1 | tkerber | a_cen_pos = np.array([0.0, 0.0, 0.0]) |
| 599 | 1 | tkerber | m_cen_pos = 0.0
|
| 600 | 1 | tkerber | for i in a.positions: |
| 601 | 1 | tkerber | a_cen_pos[0] += np.dot(directions[0], i) |
| 602 | 1 | tkerber | a_cen_pos[1] += np.dot(directions[1], i) |
| 603 | 1 | tkerber | a_cen_pos[2] += np.dot(directions[2], i) |
| 604 | 1 | tkerber | |
| 605 | 1 | tkerber | m_cen_pos = max(np.dot(-directions[2], i), m_cen_pos) |
| 606 | 1 | tkerber | a_cen_pos[0] /= len(a.positions) |
| 607 | 1 | tkerber | a_cen_pos[1] /= len(a.positions) |
| 608 | 1 | tkerber | a_cen_pos[2] /= len(a.positions) |
| 609 | 1 | tkerber | a_cen_pos[2] -= m_cen_pos
|
| 610 | 1 | tkerber | |
| 611 | 1 | tkerber | # now find the position
|
| 612 | 1 | tkerber | cen_pos = np.array([0.0, 0.0, 0.0]) |
| 613 | 1 | tkerber | if sum(self.images.selected) > 0: |
| 614 | 1 | tkerber | for i in range(len(self.R)): |
| 615 | 1 | tkerber | if self.images.selected[i]: |
| 616 | 1 | tkerber | cen_pos += self.R[i]
|
| 617 | 1 | tkerber | cen_pos /= sum(self.images.selected) |
| 618 | 1 | tkerber | elif len(self.R) > 0: |
| 619 | 1 | tkerber | px = 0.0
|
| 620 | 1 | tkerber | py = 0.0
|
| 621 | 1 | tkerber | pz = -1e6
|
| 622 | 1 | tkerber | |
| 623 | 1 | tkerber | for i in range(len(self.R)): |
| 624 | 1 | tkerber | px += np.dot(directions[0], self.R[i]) |
| 625 | 1 | tkerber | py += np.dot(directions[1], self.R[i]) |
| 626 | 1 | tkerber | pz = max(np.dot(directions[2], self.R[i]), pz) |
| 627 | 1 | tkerber | px = (px/float(len(self.R))) |
| 628 | 1 | tkerber | py = (py/float(len(self.R))) |
| 629 | 1 | tkerber | cen_pos = directions[0] * px + \
|
| 630 | 1 | tkerber | directions[1] * py + \
|
| 631 | 1 | tkerber | directions[2] * pz
|
| 632 | 1 | tkerber | |
| 633 | 1 | tkerber | if 'auto' in pos: |
| 634 | 1 | tkerber | pos = pos.replace('auto', '') |
| 635 | 1 | tkerber | import re |
| 636 | 1 | tkerber | pos = re.sub('\s', '', pos) |
| 637 | 1 | tkerber | if '(' in pos: |
| 638 | 1 | tkerber | sign = eval('%s1' % pos[0]) |
| 639 | 1 | tkerber | a_cen_pos -= sign * np.array(eval(pos[1:]), float) |
| 640 | 1 | tkerber | else:
|
| 641 | 1 | tkerber | a_cen_pos -= float(pos) * directions[2] |
| 642 | 1 | tkerber | else:
|
| 643 | 1 | tkerber | cen_pos = np.array(eval(pos))
|
| 644 | 1 | tkerber | for i in a: |
| 645 | 1 | tkerber | i.position += cen_pos - a_cen_pos |
| 646 | 1 | tkerber | |
| 647 | 1 | tkerber | # and them to the molecule
|
| 648 | 1 | tkerber | atoms = self.images.get_atoms(self.frame) |
| 649 | 1 | tkerber | atoms = atoms + a |
| 650 | 1 | tkerber | self.new_atoms(atoms, init_magmom=True) |
| 651 | 1 | tkerber | |
| 652 | 1 | tkerber | # and finally select the new molecule for easy moving and rotation
|
| 653 | 1 | tkerber | for i in range(len(a)): |
| 654 | 1 | tkerber | self.images.selected[len(atoms) - i - 1] = True |
| 655 | 1 | tkerber | |
| 656 | 1 | tkerber | self.draw()
|
| 657 | 1 | tkerber | self.add_entries[0].destroy() |
| 658 | 1 | tkerber | if data == None: |
| 659 | 1 | tkerber | molecule = ''
|
| 660 | 1 | tkerber | tag = '0'
|
| 661 | 1 | tkerber | mom = '0'
|
| 662 | 1 | tkerber | pos = 'auto+1'
|
| 663 | 1 | tkerber | self.add_entries = []
|
| 664 | 1 | tkerber | window = gtk.Window(gtk.WINDOW_TOPLEVEL) |
| 665 | 1 | tkerber | self.add_entries.append(window)
|
| 666 | 1 | tkerber | window.set_title('Add atoms')
|
| 667 | 1 | tkerber | |
| 668 | 1 | tkerber | vbox = gtk.VBox(False, 0) |
| 669 | 1 | tkerber | window.add(vbox) |
| 670 | 1 | tkerber | vbox.show() |
| 671 | 1 | tkerber | pack = False
|
| 672 | 1 | tkerber | for i, j in [['Insert atom or molecule', molecule], |
| 673 | 1 | tkerber | ['Tag', tag],
|
| 674 | 1 | tkerber | ['Moment', mom],
|
| 675 | 1 | tkerber | ['Position', pos]]:
|
| 676 | 1 | tkerber | |
| 677 | 1 | tkerber | label = gtk.Label(i) |
| 678 | 1 | tkerber | if not pack: |
| 679 | 1 | tkerber | vbox.pack_start(label, True, True, 0) |
| 680 | 1 | tkerber | else:
|
| 681 | 1 | tkerber | pack = True
|
| 682 | 1 | tkerber | vbox.add(label) |
| 683 | 1 | tkerber | label.show() |
| 684 | 1 | tkerber | |
| 685 | 1 | tkerber | entry = gtk.Entry() |
| 686 | 1 | tkerber | entry.set_text(j) |
| 687 | 1 | tkerber | self.add_entries.append(entry)
|
| 688 | 1 | tkerber | entry.set_max_length(50)
|
| 689 | 1 | tkerber | entry.show() |
| 690 | 1 | tkerber | |
| 691 | 1 | tkerber | vbox.add(entry) |
| 692 | 1 | tkerber | |
| 693 | 1 | tkerber | button = gtk.Button('_Load molecule')
|
| 694 | 1 | tkerber | button.connect('clicked', self.add_atoms, 'load') |
| 695 | 1 | tkerber | button.show() |
| 696 | 1 | tkerber | vbox.add(button) |
| 697 | 1 | tkerber | button = gtk.Button('_OK')
|
| 698 | 1 | tkerber | button.connect('clicked', self.add_atoms, 'OK') |
| 699 | 1 | tkerber | button.show() |
| 700 | 1 | tkerber | vbox.add(button) |
| 701 | 1 | tkerber | button = gtk.Button('_Cancel')
|
| 702 | 1 | tkerber | button.connect('clicked', self.add_atoms, 'Cancel') |
| 703 | 1 | tkerber | button.show() |
| 704 | 1 | tkerber | vbox.add(button) |
| 705 | 1 | tkerber | |
| 706 | 1 | tkerber | window.show() |
| 707 | 1 | tkerber | |
| 708 | 1 | tkerber | def modify_atoms(self, widget, data=None): |
| 709 | 1 | tkerber | """
|
| 710 | 1 | tkerber | Presents a dialog box where the user is able to change the atomic type, the magnetic
|
| 711 | 1 | tkerber | moment and tags of the selected atoms. An item marked with X will not be changed.
|
| 712 | 1 | tkerber | """
|
| 713 | 1 | tkerber | if data:
|
| 714 | 1 | tkerber | if data == 'OK': |
| 715 | 1 | tkerber | import ase |
| 716 | 1 | tkerber | symbol = self.add_entries[1].get_text() |
| 717 | 1 | tkerber | tag = self.add_entries[2].get_text() |
| 718 | 1 | tkerber | mom = self.add_entries[3].get_text() |
| 719 | 1 | tkerber | a = None
|
| 720 | 1 | tkerber | if symbol != 'X': |
| 721 | 1 | tkerber | try:
|
| 722 | 1 | tkerber | a = ase.Atoms([ase.Atom(symbol)]) |
| 723 | 1 | tkerber | except:
|
| 724 | 1 | tkerber | self.add_entries[1].set_text('?' + symbol) |
| 725 | 1 | tkerber | return ()
|
| 726 | 1 | tkerber | |
| 727 | 1 | tkerber | y = self.images.selected.copy()
|
| 728 | 1 | tkerber | # and them to the molecule
|
| 729 | 1 | tkerber | atoms = self.images.get_atoms(self.frame) |
| 730 | 1 | tkerber | for i in range(len(atoms)): |
| 731 | 1 | tkerber | if self.images.selected[i]: |
| 732 | 1 | tkerber | if a:
|
| 733 | 1 | tkerber | atoms[i].symbol = symbol |
| 734 | 1 | tkerber | try:
|
| 735 | 1 | tkerber | if tag != 'X': |
| 736 | 1 | tkerber | atoms[i].tag = int(tag)
|
| 737 | 1 | tkerber | except:
|
| 738 | 1 | tkerber | self.add_entries[2].set_text('?' + tag) |
| 739 | 1 | tkerber | return ()
|
| 740 | 1 | tkerber | try:
|
| 741 | 1 | tkerber | if mom != 'X': |
| 742 | 1 | tkerber | atoms[i].magmom = float(mom)
|
| 743 | 1 | tkerber | except:
|
| 744 | 1 | tkerber | self.add_entries[3].set_text('?' + mom) |
| 745 | 1 | tkerber | return ()
|
| 746 | 1 | tkerber | self.new_atoms(atoms, init_magmom=True) |
| 747 | 1 | tkerber | |
| 748 | 1 | tkerber | # and finally select the new molecule for easy moving and rotation
|
| 749 | 1 | tkerber | self.images.selected = y
|
| 750 | 1 | tkerber | self.draw()
|
| 751 | 1 | tkerber | |
| 752 | 1 | tkerber | self.add_entries[0].destroy() |
| 753 | 1 | tkerber | if data == None and sum(self.images.selected): |
| 754 | 1 | tkerber | atoms = self.images.get_atoms(self.frame) |
| 755 | 1 | tkerber | s_tag = ''
|
| 756 | 1 | tkerber | s_mom = ''
|
| 757 | 1 | tkerber | s_symbol = ''
|
| 758 | 1 | tkerber | # Get the tags, moments and symbols of the selected atomsa
|
| 759 | 1 | tkerber | for i in range(len(atoms)): |
| 760 | 1 | tkerber | if self.images.selected[i]: |
| 761 | 1 | tkerber | if not(s_tag): |
| 762 | 1 | tkerber | s_tag = str(atoms[i].tag)
|
| 763 | 1 | tkerber | elif s_tag != str(atoms[i].tag): |
| 764 | 1 | tkerber | s_tag = 'X'
|
| 765 | 1 | tkerber | if not(s_mom): |
| 766 | 1 | tkerber | s_mom = ("%2.2f" % (atoms[i].magmom))
|
| 767 | 1 | tkerber | elif s_mom != ("%2.2f" % (atoms[i].magmom)): |
| 768 | 1 | tkerber | s_mom = 'X'
|
| 769 | 1 | tkerber | if not(s_symbol): |
| 770 | 1 | tkerber | s_symbol = str(atoms[i].symbol)
|
| 771 | 1 | tkerber | elif s_symbol != str(atoms[i].symbol): |
| 772 | 1 | tkerber | s_symbol = 'X'
|
| 773 | 1 | tkerber | |
| 774 | 1 | tkerber | self.add_entries = []
|
| 775 | 1 | tkerber | window = gtk.Window(gtk.WINDOW_TOPLEVEL) |
| 776 | 1 | tkerber | self.add_entries.append(window)
|
| 777 | 1 | tkerber | window.set_title('Modify')
|
| 778 | 1 | tkerber | |
| 779 | 1 | tkerber | vbox = gtk.VBox(False, 0) |
| 780 | 1 | tkerber | window.add(vbox) |
| 781 | 1 | tkerber | vbox.show() |
| 782 | 1 | tkerber | pack = False
|
| 783 | 1 | tkerber | for i, j in [['Atom', s_symbol], |
| 784 | 1 | tkerber | ['Tag', s_tag],
|
| 785 | 1 | tkerber | ['Moment', s_mom]]:
|
| 786 | 1 | tkerber | label = gtk.Label(i) |
| 787 | 1 | tkerber | if not pack: |
| 788 | 1 | tkerber | vbox.pack_start(label, True, True, 0) |
| 789 | 1 | tkerber | else:
|
| 790 | 1 | tkerber | pack = True
|
| 791 | 1 | tkerber | vbox.add(label) |
| 792 | 1 | tkerber | label.show() |
| 793 | 1 | tkerber | |
| 794 | 1 | tkerber | entry = gtk.Entry() |
| 795 | 1 | tkerber | entry.set_text(j) |
| 796 | 1 | tkerber | self.add_entries.append(entry)
|
| 797 | 1 | tkerber | entry.set_max_length(50)
|
| 798 | 1 | tkerber | entry.show() |
| 799 | 1 | tkerber | vbox.add(entry) |
| 800 | 1 | tkerber | button = gtk.Button('_OK')
|
| 801 | 1 | tkerber | button.connect('clicked', self.modify_atoms, 'OK') |
| 802 | 1 | tkerber | button.show() |
| 803 | 1 | tkerber | vbox.add(button) |
| 804 | 1 | tkerber | button = gtk.Button('_Cancel')
|
| 805 | 1 | tkerber | button.connect('clicked', self.modify_atoms, 'Cancel') |
| 806 | 1 | tkerber | button.show() |
| 807 | 1 | tkerber | vbox.add(button) |
| 808 | 1 | tkerber | |
| 809 | 1 | tkerber | window.show() |
| 810 | 1 | tkerber | |
| 811 | 1 | tkerber | def delete_selected_atoms(self, widget, data=None): |
| 812 | 1 | tkerber | if data == 'OK': |
| 813 | 1 | tkerber | atoms = self.images.get_atoms(self.frame) |
| 814 | 1 | tkerber | lena = len(atoms)
|
| 815 | 1 | tkerber | for i in range(len(atoms)): |
| 816 | 1 | tkerber | li = lena-1-i
|
| 817 | 1 | tkerber | if self.images.selected[li]: |
| 818 | 1 | tkerber | del(atoms[li])
|
| 819 | 1 | tkerber | self.new_atoms(atoms)
|
| 820 | 1 | tkerber | |
| 821 | 1 | tkerber | self.draw()
|
| 822 | 1 | tkerber | if data:
|
| 823 | 1 | tkerber | self.window.destroy()
|
| 824 | 1 | tkerber | |
| 825 | 1 | tkerber | if not(data) and sum(self.images.selected): |
| 826 | 1 | tkerber | more = '' + (sum(self.images.selected) > 1) * 's' |
| 827 | 1 | tkerber | self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
|
| 828 | 1 | tkerber | self.window.set_title('Confirmation') |
| 829 | 1 | tkerber | self.window.set_border_width(10) |
| 830 | 1 | tkerber | self.box1 = gtk.HBox(False, 0) |
| 831 | 1 | tkerber | self.window.add(self.box1) |
| 832 | 1 | tkerber | self.button1 = gtk.Button('Delete selected atom%s?' % more) |
| 833 | 1 | tkerber | self.button1.connect("clicked", self.delete_selected_atoms, "OK") |
| 834 | 1 | tkerber | self.box1.pack_start(self.button1, True, True, 0) |
| 835 | 1 | tkerber | self.button1.show()
|
| 836 | 1 | tkerber | |
| 837 | 1 | tkerber | self.button2 = gtk.Button("Cancel") |
| 838 | 1 | tkerber | self.button2.connect("clicked", self.delete_selected_atoms, "Cancel") |
| 839 | 1 | tkerber | self.box1.pack_start(self.button2, True, True, 0) |
| 840 | 1 | tkerber | self.button2.show()
|
| 841 | 1 | tkerber | |
| 842 | 1 | tkerber | self.box1.show()
|
| 843 | 1 | tkerber | self.window.show()
|
| 844 | 1 | tkerber | |
| 845 | 1 | tkerber | def debug(self, x): |
| 846 | 1 | tkerber | from ase.gui.debug import Debug |
| 847 | 1 | tkerber | Debug(self)
|
| 848 | 1 | tkerber | |
| 849 | 1 | tkerber | def execute(self, widget=None): |
| 850 | 1 | tkerber | from ase.gui.execute import Execute |
| 851 | 1 | tkerber | Execute(self)
|
| 852 | 1 | tkerber | |
| 853 | 1 | tkerber | def constraints_window(self, widget=None): |
| 854 | 1 | tkerber | from ase.gui.constraints import Constraints |
| 855 | 1 | tkerber | Constraints(self)
|
| 856 | 1 | tkerber | |
| 857 | 1 | tkerber | def dft_window(self, widget=None): |
| 858 | 1 | tkerber | from ase.gui.dft import DFT |
| 859 | 1 | tkerber | DFT(self)
|
| 860 | 1 | tkerber | |
| 861 | 1 | tkerber | def select_all(self, widget): |
| 862 | 1 | tkerber | self.images.selected[:] = True |
| 863 | 1 | tkerber | self.draw()
|
| 864 | 1 | tkerber | |
| 865 | 1 | tkerber | def invert_selection(self, widget): |
| 866 | 1 | tkerber | self.images.selected[:] = ~self.images.selected |
| 867 | 1 | tkerber | self.draw()
|
| 868 | 1 | tkerber | |
| 869 | 1 | tkerber | def select_constrained_atoms(self, widget): |
| 870 | 1 | tkerber | self.images.selected[:] = ~self.images.dynamic |
| 871 | 1 | tkerber | self.draw()
|
| 872 | 1 | tkerber | |
| 873 | 1 | tkerber | def movie(self, widget=None): |
| 874 | 1 | tkerber | from ase.gui.movie import Movie |
| 875 | 1 | tkerber | self.movie_window = Movie(self) |
| 876 | 1 | tkerber | |
| 877 | 1 | tkerber | def plot_graphs(self, x=None, expr=None): |
| 878 | 1 | tkerber | from ase.gui.graphs import Graphs |
| 879 | 1 | tkerber | g = Graphs(self)
|
| 880 | 1 | tkerber | if expr is not None: |
| 881 | 1 | tkerber | g.plot(expr=expr) |
| 882 | 1 | tkerber | self.graph_wref.append(weakref.ref(g))
|
| 883 | 1 | tkerber | |
| 884 | 1 | tkerber | def plot_graphs_newatoms(self): |
| 885 | 1 | tkerber | "Notify any Graph objects that they should make new plots."
|
| 886 | 1 | tkerber | new_wref = [] |
| 887 | 1 | tkerber | found = 0
|
| 888 | 1 | tkerber | for wref in self.graph_wref: |
| 889 | 1 | tkerber | ref = wref() |
| 890 | 1 | tkerber | if ref is not None: |
| 891 | 1 | tkerber | ref.plot() |
| 892 | 1 | tkerber | new_wref.append(wref) # Preserve weakrefs that still work.
|
| 893 | 1 | tkerber | found += 1
|
| 894 | 1 | tkerber | self.graph_wref = new_wref
|
| 895 | 1 | tkerber | return found
|
| 896 | 1 | tkerber | |
| 897 | 1 | tkerber | def NEB(self, action): |
| 898 | 1 | tkerber | from ase.gui.neb import NudgedElasticBand |
| 899 | 1 | tkerber | NudgedElasticBand(self.images)
|
| 900 | 1 | tkerber | |
| 901 | 1 | tkerber | def bulk_modulus(self, action): |
| 902 | 1 | tkerber | from ase.gui.bulk_modulus import BulkModulus |
| 903 | 1 | tkerber | BulkModulus(self.images)
|
| 904 | 1 | tkerber | |
| 905 | 1 | tkerber | def open(self, button=None, filenames=None): |
| 906 | 1 | tkerber | if filenames == None: |
| 907 | 1 | tkerber | chooser = gtk.FileChooserDialog( |
| 908 | 1 | tkerber | _('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 909 | 1 | tkerber | (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 910 | 1 | tkerber | gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 911 | 1 | tkerber | ok = chooser.run() == gtk.RESPONSE_OK |
| 912 | 1 | tkerber | if ok:
|
| 913 | 1 | tkerber | filenames = [chooser.get_filename()] |
| 914 | 1 | tkerber | chooser.destroy() |
| 915 | 1 | tkerber | |
| 916 | 1 | tkerber | if not ok: |
| 917 | 1 | tkerber | return
|
| 918 | 1 | tkerber | |
| 919 | 1 | tkerber | self.reset_tools_modes()
|
| 920 | 1 | tkerber | self.images.read(filenames, slice(None)) |
| 921 | 1 | tkerber | self.set_colors()
|
| 922 | 1 | tkerber | self.set_coordinates(self.images.nimages - 1, focus=True) |
| 923 | 1 | tkerber | |
| 924 | 1 | tkerber | def import_atoms (self, button=None, filenames=None): |
| 925 | 1 | tkerber | if filenames == None: |
| 926 | 1 | tkerber | chooser = gtk.FileChooserDialog( |
| 927 | 1 | tkerber | _('Open ...'), None, gtk.FILE_CHOOSER_ACTION_OPEN, |
| 928 | 1 | tkerber | (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 929 | 1 | tkerber | gtk.STOCK_OPEN, gtk.RESPONSE_OK)) |
| 930 | 1 | tkerber | ok = chooser.run() |
| 931 | 1 | tkerber | if ok == gtk.RESPONSE_OK:
|
| 932 | 1 | tkerber | filenames = [chooser.get_filename()] |
| 933 | 1 | tkerber | chooser.destroy() |
| 934 | 1 | tkerber | |
| 935 | 1 | tkerber | if not ok: |
| 936 | 1 | tkerber | return
|
| 937 | 1 | tkerber | |
| 938 | 1 | tkerber | |
| 939 | 1 | tkerber | self.images.import_atoms(filenames, self.frame) |
| 940 | 1 | tkerber | self.set_colors()
|
| 941 | 1 | tkerber | self.set_coordinates(self.images.nimages - 1, focus=True) |
| 942 | 1 | tkerber | |
| 943 | 1 | tkerber | def save(self, action): |
| 944 | 1 | tkerber | chooser = gtk.FileChooserDialog( |
| 945 | 1 | tkerber | _('Save ...'), None, gtk.FILE_CHOOSER_ACTION_SAVE, |
| 946 | 1 | tkerber | (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, |
| 947 | 1 | tkerber | gtk.STOCK_SAVE, gtk.RESPONSE_OK)) |
| 948 | 1 | tkerber | |
| 949 | 1 | tkerber | # Add a file type filter
|
| 950 | 1 | tkerber | types = [] |
| 951 | 1 | tkerber | name_to_suffix = {}
|
| 952 | 1 | tkerber | for name, suffix in [('Automatic', None), |
| 953 | 1 | tkerber | ('XYZ file', 'xyz'), |
| 954 | 1 | tkerber | ('ASE trajectory', 'traj'), |
| 955 | 1 | tkerber | ('PDB file', 'pdb'), |
| 956 | 1 | tkerber | ('Gaussian cube file', 'cube'), |
| 957 | 1 | tkerber | ('Python script', 'py'), |
| 958 | 1 | tkerber | ('VNL file', 'vnl'), |
| 959 | 1 | tkerber | ('Portable Network Graphics', 'png'), |
| 960 | 1 | tkerber | ('Persistance of Vision', 'pov'), |
| 961 | 1 | tkerber | ('Encapsulated PostScript', 'eps'), |
| 962 | 1 | tkerber | ('FHI-aims geometry input', 'in'), |
| 963 | 1 | tkerber | ('VASP geometry input', 'POSCAR')]: |
| 964 | 1 | tkerber | if suffix is None: |
| 965 | 1 | tkerber | name = _(name) |
| 966 | 1 | tkerber | else:
|
| 967 | 1 | tkerber | name = '%s (%s)' % (_(name), suffix)
|
| 968 | 1 | tkerber | filt = gtk.FileFilter() |
| 969 | 1 | tkerber | filt.set_name(name) |
| 970 | 1 | tkerber | if suffix is None: |
| 971 | 1 | tkerber | filt.add_pattern('*')
|
| 972 | 1 | tkerber | elif suffix == 'POSCAR': |
| 973 | 1 | tkerber | filt.add_pattern('*POSCAR*')
|
| 974 | 1 | tkerber | else:
|
| 975 | 1 | tkerber | filt.add_pattern('*.'+suffix)
|
| 976 | 1 | tkerber | if suffix is not None: |
| 977 | 1 | tkerber | types.append(suffix) |
| 978 | 1 | tkerber | name_to_suffix[name] = suffix |
| 979 | 1 | tkerber | |
| 980 | 1 | tkerber | chooser.add_filter(filt) |
| 981 | 1 | tkerber | |
| 982 | 1 | tkerber | if self.images.nimages > 1: |
| 983 | 1 | tkerber | img_vbox = gtk.VBox() |
| 984 | 1 | tkerber | button = gtk.CheckButton('Save current image only (#%d)' %
|
| 985 | 1 | tkerber | self.frame)
|
| 986 | 1 | tkerber | pack(img_vbox, button) |
| 987 | 1 | tkerber | entry = gtk.Entry(10)
|
| 988 | 1 | tkerber | pack(img_vbox, [gtk.Label(_('Slice: ')), entry,
|
| 989 | 1 | tkerber | help('Help for slice ...')])
|
| 990 | 1 | tkerber | entry.set_text('0:%d' % self.images.nimages) |
| 991 | 1 | tkerber | img_vbox.show() |
| 992 | 1 | tkerber | chooser.set_extra_widget(img_vbox) |
| 993 | 1 | tkerber | |
| 994 | 1 | tkerber | while True: |
| 995 | 1 | tkerber | # Loop until the user selects a proper file name, or cancels.
|
| 996 | 1 | tkerber | response = chooser.run() |
| 997 | 1 | tkerber | if response == gtk.RESPONSE_CANCEL:
|
| 998 | 1 | tkerber | chooser.destroy() |
| 999 | 1 | tkerber | return
|
| 1000 | 1 | tkerber | elif response != gtk.RESPONSE_OK:
|
| 1001 | 1 | tkerber | print >>sys.stderr, "AG INTERNAL ERROR: strange response in Save,", response |
| 1002 | 1 | tkerber | chooser.destroy() |
| 1003 | 1 | tkerber | return
|
| 1004 | 1 | tkerber | |
| 1005 | 1 | tkerber | filename = chooser.get_filename() |
| 1006 | 1 | tkerber | |
| 1007 | 1 | tkerber | suffix = os.path.splitext(filename)[1][1:] |
| 1008 | 1 | tkerber | if 'POSCAR' in filename: |
| 1009 | 1 | tkerber | suffix = 'POSCAR'
|
| 1010 | 1 | tkerber | if suffix == '': |
| 1011 | 1 | tkerber | # No suffix given. If the user has chosen a special
|
| 1012 | 1 | tkerber | # file type, use the corresponding suffix.
|
| 1013 | 1 | tkerber | filt = chooser.get_filter().get_name() |
| 1014 | 1 | tkerber | suffix = name_to_suffix[filt] |
| 1015 | 1 | tkerber | filename = filename + '.' + suffix
|
| 1016 | 1 | tkerber | |
| 1017 | 1 | tkerber | if suffix not in types: |
| 1018 | 1 | tkerber | oops(message='Unknown output format!',
|
| 1019 | 1 | tkerber | message2='Use one of: ' + ', '.join(types[1:])) |
| 1020 | 1 | tkerber | continue
|
| 1021 | 1 | tkerber | |
| 1022 | 1 | tkerber | if self.images.nimages > 1: |
| 1023 | 1 | tkerber | if button.get_active():
|
| 1024 | 1 | tkerber | filename += '@%d' % self.frame |
| 1025 | 1 | tkerber | else:
|
| 1026 | 1 | tkerber | filename += '@' + entry.get_text()
|
| 1027 | 1 | tkerber | |
| 1028 | 1 | tkerber | break
|
| 1029 | 1 | tkerber | |
| 1030 | 1 | tkerber | chooser.destroy() |
| 1031 | 1 | tkerber | |
| 1032 | 1 | tkerber | bbox = np.empty(4)
|
| 1033 | 1 | tkerber | size = np.array([self.width, self.height]) / self.scale |
| 1034 | 1 | tkerber | bbox[0:2] = np.dot(self.center, self.axes[:, :2]) - size / 2 |
| 1035 | 1 | tkerber | bbox[2:] = bbox[:2] + size |
| 1036 | 1 | tkerber | suc = self.ui.get_widget('/MenuBar/ViewMenu/ShowUnitCell').get_active() |
| 1037 | 1 | tkerber | self.images.write(filename, self.axes, show_unit_cell=suc, bbox=bbox) |
| 1038 | 1 | tkerber | |
| 1039 | 1 | tkerber | def bulk_window(self, menuitem): |
| 1040 | 1 | tkerber | SetupBulkCrystal(self)
|
| 1041 | 1 | tkerber | |
| 1042 | 1 | tkerber | def surface_window(self, menuitem): |
| 1043 | 1 | tkerber | SetupSurfaceSlab(self)
|
| 1044 | 1 | tkerber | |
| 1045 | 1 | tkerber | def nanoparticle_window(self, menuitem): |
| 1046 | 1 | tkerber | SetupNanoparticle(self)
|
| 1047 | 1 | tkerber | |
| 1048 | 1 | tkerber | def graphene_window(self, menuitem): |
| 1049 | 1 | tkerber | SetupGraphene(self)
|
| 1050 | 1 | tkerber | |
| 1051 | 1 | tkerber | def nanotube_window(self, menuitem): |
| 1052 | 1 | tkerber | SetupNanotube(self)
|
| 1053 | 1 | tkerber | |
| 1054 | 1 | tkerber | def calculator_window(self, menuitem): |
| 1055 | 1 | tkerber | SetCalculator(self)
|
| 1056 | 1 | tkerber | |
| 1057 | 1 | tkerber | def energy_window(self, menuitem): |
| 1058 | 1 | tkerber | EnergyForces(self)
|
| 1059 | 1 | tkerber | |
| 1060 | 1 | tkerber | def energy_minimize_window(self, menuitem): |
| 1061 | 1 | tkerber | Minimize(self)
|
| 1062 | 1 | tkerber | |
| 1063 | 1 | tkerber | def scaling_window(self, menuitem): |
| 1064 | 1 | tkerber | HomogeneousDeformation(self)
|
| 1065 | 1 | tkerber | |
| 1066 | 1 | tkerber | def new_atoms(self, atoms, init_magmom=False): |
| 1067 | 1 | tkerber | "Set a new atoms object."
|
| 1068 | 1 | tkerber | self.notify_vulnerable()
|
| 1069 | 1 | tkerber | self.reset_tools_modes()
|
| 1070 | 1 | tkerber | |
| 1071 | 1 | tkerber | rpt = getattr(self.images, 'repeat', None) |
| 1072 | 1 | tkerber | self.images.repeat_images(np.ones(3, int)) |
| 1073 | 1 | tkerber | self.images.initialize([atoms], init_magmom=init_magmom)
|
| 1074 | 1 | tkerber | self.frame = 0 # Prevent crashes |
| 1075 | 1 | tkerber | self.images.repeat_images(rpt)
|
| 1076 | 1 | tkerber | self.set_colors()
|
| 1077 | 1 | tkerber | self.set_coordinates(frame=0, focus=True) |
| 1078 | 1 | tkerber | |
| 1079 | 1 | tkerber | def prepare_new_atoms(self): |
| 1080 | 1 | tkerber | "Marks that the next call to append_atoms should clear the images."
|
| 1081 | 1 | tkerber | self.images.prepare_new_atoms()
|
| 1082 | 1 | tkerber | |
| 1083 | 1 | tkerber | def append_atoms(self, atoms): |
| 1084 | 1 | tkerber | "Set a new atoms object."
|
| 1085 | 1 | tkerber | #self.notify_vulnerable() # Do this manually after last frame.
|
| 1086 | 1 | tkerber | frame = self.images.append_atoms(atoms)
|
| 1087 | 1 | tkerber | self.set_coordinates(frame=frame-1, focus=True) |
| 1088 | 1 | tkerber | |
| 1089 | 1 | tkerber | def notify_vulnerable(self): |
| 1090 | 1 | tkerber | """Notify windows that would break when new_atoms is called.
|
| 1091 | 1 | tkerber |
|
| 1092 | 1 | tkerber | The notified windows may adapt to the new atoms. If that is not
|
| 1093 | 1 | tkerber | possible, they should delete themselves.
|
| 1094 | 1 | tkerber | """
|
| 1095 | 1 | tkerber | new_vul = [] # Keep weakrefs to objects that still exist.
|
| 1096 | 1 | tkerber | for wref in self.vulnerable_windows: |
| 1097 | 1 | tkerber | ref = wref() |
| 1098 | 1 | tkerber | if ref is not None: |
| 1099 | 1 | tkerber | new_vul.append(wref) |
| 1100 | 1 | tkerber | ref.notify_atoms_changed() |
| 1101 | 1 | tkerber | self.vulnerable_windows = new_vul
|
| 1102 | 1 | tkerber | |
| 1103 | 1 | tkerber | def register_vulnerable(self, obj): |
| 1104 | 1 | tkerber | """Register windows that are vulnerable to changing the images.
|
| 1105 | 1 | tkerber |
|
| 1106 | 1 | tkerber | Some windows will break if the atoms (and in particular the
|
| 1107 | 1 | tkerber | number of images) are changed. They can register themselves
|
| 1108 | 1 | tkerber | and be closed when that happens.
|
| 1109 | 1 | tkerber | """
|
| 1110 | 1 | tkerber | self.vulnerable_windows.append(weakref.ref(obj))
|
| 1111 | 1 | tkerber | |
| 1112 | 1 | tkerber | def exit(self, button, event=None): |
| 1113 | 1 | tkerber | gtk.main_quit() |
| 1114 | 1 | tkerber | return True |
| 1115 | 1 | tkerber | |
| 1116 | 1 | tkerber | def xxx(self, x=None, |
| 1117 | 1 | tkerber | message1='Not implemented!',
|
| 1118 | 1 | tkerber | message2='do you really need it?'):
|
| 1119 | 1 | tkerber | oops(message1, message2) |
| 1120 | 1 | tkerber | |
| 1121 | 1 | tkerber | def about(self, action): |
| 1122 | 1 | tkerber | try:
|
| 1123 | 1 | tkerber | dialog = gtk.AboutDialog() |
| 1124 | 1 | tkerber | except AttributeError: |
| 1125 | 1 | tkerber | self.xxx()
|
| 1126 | 1 | tkerber | else:
|
| 1127 | 1 | tkerber | dialog.run() |
| 1128 | 1 | tkerber | |
| 1129 | 1 | tkerber | def webpage(widget): |
| 1130 | 1 | tkerber | import webbrowser |
| 1131 | 1 | tkerber | webbrowser.open('https://wiki.fysik.dtu.dk/ase/ase/gui.html')
|