Class: AimsProject::CrystalViewer

Inherits:
Wx::Panel
  • Object
show all
Includes:
Aims, Gl, Glu, Math, Wx
Defined in:
lib/aims_project/crystal_viewer.rb

Constant Summary collapse

ID_ROTATE = 
100
ID_PAN = 
101
ID_ZOOM = 
102
PICK_ID_ATOM = 
0x10000000
PICK_ID_PLANE = 
0x20000000
PICK_ID_BOND = 
0x30000000

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(controller, parent, options = nil) ⇒ CrystalViewer

Returns a new instance of CrystalViewer.



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# File 'lib/aims_project/crystal_viewer.rb', line 50

def initialize(controller, parent, options = nil)

  super(parent)
  @controller = controller
  
  # Register self as an observer of the options
  if options
    @options = options
  else
    @options = CrystalViewerOptions.new(parent)
  end 
  @options.add_observer(self)

  # Toolbar for the GL Canvas
  basedir = File.dirname(__FILE__)
  rotate_icon = Image.new(File.join(basedir,"rotate.gif"), BITMAP_TYPE_GIF)
  @rotate_tool = BitmapButton.new(self, :id => ID_ROTATE, :bitmap => rotate_icon.rescale(16,15).convert_to_bitmap,:name => "rotate")
  
  zoom_icon = Image.new(File.join(basedir,"zoom.gif"), BITMAP_TYPE_GIF)
  @zoom_tool = BitmapButton.new(self, :id => ID_ZOOM, :bitmap => zoom_icon.rescale(16,15).convert_to_bitmap, :name => "zoom")
  
  pan_icon = Image.new(File.join(basedir,"pan.gif"), BITMAP_TYPE_GIF)
  @pan_tool = BitmapButton.new(self, :id => ID_PAN, :bitmap => pan_icon.rescale(16,15).convert_to_bitmap, :name => "pan")

  evt_button(@rotate_tool) {|evt|
    set_mouse_motion_function(:rotate)
  }

  evt_button(@zoom_tool) {|evt|
    set_mouse_motion_function(:zoom)
  }

  evt_button(@pan_tool) {|evt|
    set_mouse_motion_function(:pan)
  }

  @buttonSizer = HBoxSizer.new
  @buttonSizer.add_item(@rotate_tool)
  @buttonSizer.add_item(@zoom_tool)
  @buttonSizer.add_item(@pan_tool)


  #@glPanel = CalendarCtrl.new(self)
  attrib = [Wx::GL_RGBA, Wx::GL_DOUBLEBUFFER, Wx::GL_DEPTH_SIZE, 24]
  @glPanel = GLCanvas.new(self, -1, [-1, -1], [-1, -1],
                             Wx::FULL_REPAINT_ON_RESIZE, "GLCanvas", attrib)
  
  vbox_sizer = VBoxSizer.new
  vbox_sizer.add_item(@buttonSizer, :flag => EXPAND)
  vbox_sizer.add_item(@glPanel, :proportion => 1, :flag => EXPAND)
  set_sizer(vbox_sizer)
  

  set_defaults
  
  # Define the method to call for paint requests
  evt_paint { @glPanel.paint { draw_scene }}
  # Create the graphics view and define event handlers

  # For some reason, not all left-clicks are captured, 
  # so we include this catchall as well, to prevent odd
  # behavior when rotating
  @glPanel.evt_mouse_events {|evt|
    if evt.button_down
      self.set_focus
      mouse_down(evt.get_x, evt.get_y)
    end
  }
  
  @glPanel.evt_left_up {|evt|
    mouse_up(evt.get_x, evt.get_y)
    draw_scene
  }
  
  @glPanel.evt_motion {|evt|
    if evt.dragging
      mouse_dragged(evt.get_x, evt.get_y)
      draw_scene
    end
  }
  
  @glPanel.evt_char {|evt| 
    nudge_dir = case evt.get_key_code
        when K_LEFT
          [-1,0,0]
        when K_RIGHT
          [1,0,0]
        when K_UP
          [0,1,0]
        when K_DOWN
          [0,-1,0]
        else
          [0,0,0]
        end
      nudge(nudge_dir)
  }
  
    # What to do when worker threads return
    evt_thread_callback {|evt|
      self.draw_scene
    }
end

Instance Attribute Details

#alt ⇒ Object

Returns the value of attribute alt.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def alt
  @alt
end

#atom ⇒ Object

Returns the value of attribute atom.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def atom
  @atom
end

#atoms_changed ⇒ Object

Returns the value of attribute atoms_changed.



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# File 'lib/aims_project/crystal_viewer.rb', line 46

def atoms_changed
  @atoms_changed
end

#az ⇒ Object

Returns the value of attribute az.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def az
  @az
end

#background ⇒ Object

The background color (glClearColor)



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# File 'lib/aims_project/crystal_viewer.rb', line 33

def background
  @background
end

#current_cell ⇒ Object

If displaying multiple, then the current cell



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# File 'lib/aims_project/crystal_viewer.rb', line 27

def current_cell
  @current_cell
end

#height ⇒ Object

Returns the value of attribute height.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def height
  @height
end

#mouse_motion_func ⇒ Object

The keyboard actions



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# File 'lib/aims_project/crystal_viewer.rb', line 30

def mouse_motion_func
  @mouse_motion_func
end

#offx ⇒ Object

Returns the value of attribute offx.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def offx
  @offx
end

#offy ⇒ Object

Returns the value of attribute offy.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def offy
  @offy
end

#offz ⇒ Object

Returns the value of attribute offz.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def offz
  @offz
end

#ortho_side ⇒ Object

Returns the value of attribute ortho_side.



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# File 'lib/aims_project/crystal_viewer.rb', line 35

def ortho_side
  @ortho_side
end

#ortho_zmax ⇒ Object

Returns the value of attribute ortho_zmax.



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# File 'lib/aims_project/crystal_viewer.rb', line 35

def ortho_zmax
  @ortho_zmax
end

#ortho_zmin ⇒ Object

Returns the value of attribute ortho_zmin.



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# File 'lib/aims_project/crystal_viewer.rb', line 35

def ortho_zmin
  @ortho_zmin
end

#orthographic ⇒ Object

Returns the value of attribute orthographic.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def orthographic
  @orthographic
end

#picking ⇒ Object

Returns the value of attribute picking.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def picking
  @picking
end

#render_mode ⇒ Object

Returns the value of attribute render_mode.



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# File 'lib/aims_project/crystal_viewer.rb', line 38

def render_mode
  @render_mode
end

#repeat ⇒ Object

How many times to repeat the unit cell A three element vector



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# File 'lib/aims_project/crystal_viewer.rb', line 24

def repeat
  @repeat
end

#selection ⇒ Object

Returns the value of attribute selection.



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# File 'lib/aims_project/crystal_viewer.rb', line 48

def selection
  @selection
end

#slices ⇒ Object

Returns the value of attribute slices.



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# File 'lib/aims_project/crystal_viewer.rb', line 44

def slices
  @slices
end

#stacks ⇒ Object

Returns the value of attribute stacks.



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# File 'lib/aims_project/crystal_viewer.rb', line 44

def stacks
  @stacks
end

#unit_cell ⇒ Object

An array of Aims::UnitCell’s to display



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# File 'lib/aims_project/crystal_viewer.rb', line 19

def unit_cell
  @unit_cell
end

#unit_cell_corrected ⇒ Object (readonly)

Returns the value of attribute unit_cell_corrected.



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# File 'lib/aims_project/crystal_viewer.rb', line 20

def unit_cell_corrected
  @unit_cell_corrected
end

#width ⇒ Object

Returns the value of attribute width.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def width
  @width
end

#x_down ⇒ Object

Returns the value of attribute x_down.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def x_down
  @x_down
end

#x_last ⇒ Object

Returns the value of attribute x_last.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def x_last
  @x_last
end

#xmax_plane ⇒ Object

Returns the value of attribute xmax_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 40

def xmax_plane
  @xmax_plane
end

#xmin_plane ⇒ Object

Returns the value of attribute xmin_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 40

def xmin_plane
  @xmin_plane
end

#y_down ⇒ Object

Returns the value of attribute y_down.



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# File 'lib/aims_project/crystal_viewer.rb', line 36

def y_down
  @y_down
end

#y_last ⇒ Object

Returns the value of attribute y_last.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def y_last
  @y_last
end

#ymax_plane ⇒ Object

Returns the value of attribute ymax_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 41

def ymax_plane
  @ymax_plane
end

#ymin_plane ⇒ Object

Returns the value of attribute ymin_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 41

def ymin_plane
  @ymin_plane
end

#z_last ⇒ Object

Returns the value of attribute z_last.



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# File 'lib/aims_project/crystal_viewer.rb', line 37

def z_last
  @z_last
end

#zmax_plane ⇒ Object

Returns the value of attribute zmax_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 42

def zmax_plane
  @zmax_plane
end

#zmin_plane ⇒ Object

Returns the value of attribute zmin_plane.



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# File 'lib/aims_project/crystal_viewer.rb', line 42

def zmin_plane
  @zmin_plane
end

Instance Method Details

#add_lights ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 636

def add_lights
  light0_position = [1,1,1,0]
  light1_position = [-1,-1,1,1]
  glLightModel(GL_LIGHT_MODEL_AMBIENT, [0.6, 0.6, 0.6 ,1.0])
  # glLightModel(GL_LIGHT_MODEL_LOCAL_VIEWER, GL_TRUE)
  glLightfv(GL_LIGHT0, GL_POSITION, light0_position)              
  glLightfv(GL_LIGHT1, GL_POSITION, light1_position)
end

#alpha_image_data ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 976

def alpha_image_data
  # 1 byte/pixel
  bytewidth = self.width;
  
  bytes = bytewidth*height;
  @glPanel.set_current
  glFinish

  # Setup pixel store
  glPixelStorei(Gl::GL_PACK_ALIGNMENT, 1) # Force byte alignment
  glPixelStorei(Gl::GL_PACK_ROW_LENGTH, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_ROWS, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_PIXELS, 0)
  
  glReadPixels(0, 0, self.width, self.height, Gl::GL_ALPHA, Gl::GL_UNSIGNED_BYTE)
end

#apply_projection ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 509

def apply_projection
  glMatrixMode(GL_PROJECTION)
  glLoadIdentity()
  if self.orthographic
    glOrtho(-self.ortho_side, self.ortho_side, -self.ortho_side,self.ortho_side, self.ortho_zmin, self.ortho_zmax)
  else
    gluPerspective(60, self.width/self.height, 1, 120)
  end
  glMatrixMode(GL_MODELVIEW)
end

#bond_length=(l) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 283

def bond_length=(l)
  @options.bond_length = l
  # FIXME The bonds should be made in the controller
  # self.unit_cell.each{|uc| uc.make_bonds(l)} if self.unit_cell
end

#cast_ray_to(x, y) ⇒ Object

Cast a ray from the near clip-plane to the far clip-plane through the point x,y return a two element array

element 0 is the model space coordinates of (x,y) on the near clip plane 
element 1 is the direction of the ray



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# File 'lib/aims_project/crystal_viewer.rb', line 380

def cast_ray_to(x,y)
  x1,y1,z1 = unproject(x,y,0)
  x2,y2,z2 = unproject(x,y,1)
  [ Vector[x1, y1, z1], Vector[x2-x1, y2-y1, z2-z1] ]
end

#current_unit_cell ⇒ Object

The currently displayed unit cell



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# File 'lib/aims_project/crystal_viewer.rb', line 272

def current_unit_cell
  self.unit_cell
end

#delete_atom ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 359

def delete_atom
  if self.atom
    # Remove 
    self.unit_cell.remove_atom(self.atom)
  end
end

#draw_bonds(origin = [0,0,0]) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 713

def draw_bonds(origin = [0,0,0])
  return unless self.unit_cell
  atoms = if @options.correct
    @unit_cell_corrected
  else
      @unit_cell
  end
  return unless atoms.bonds

  Material.black.apply
  glLineWidth(1.0)
  glBegin(GL_LINES)
  atoms.bonds.each{|b|
    glVertex3f(origin[0] + b[0].x, origin[1] + b[0].y, origin[2] + b[0].z)
    glVertex3f(origin[0] + b[1].x, origin[1] + b[1].y, origin[2] + b[1].z)				
  }
  glEnd()
end

#draw_clip_planes ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 869

def draw_clip_planes
  return unless self.unit_cell
  atoms = self.unit_cell

  bb = atoms.bounding_box
  bbx1 = bb[0].x
  bbx2 = bb[1].x
  bby1 = bb[0].y
  bby2 = bb[1].y
  bbz1 = bb[0].z
  bbz2 = bb[1].z

  # draw z_planes
  # The are bounded by the min and max points in the x-y plane

  if @options.show_zclip and @zmax_plane and @zmin_plane
    z = -1*@zmax_plane.distance_to_point(0,0,0)
    draw_plane(@zmax_plane, [[bbx1, bby1, z],
                             [bbx2, bby1, z],
                             [bbx2, bby2, z], 
                             [bbx1, bby2, z]],1)

     z = @zmin_plane.distance_to_point(0,0,0)
     draw_plane(@zmin_plane, [[bbx1, bby1, z],
                              [bbx2, bby1, z],
                              [bbx2, bby2, z], 
                              [bbx1, bby2, z]],2)
  end

  if @options.show_xclip and @xmax_plane and @xmin_plane
    x = -1*@xmax_plane.distance_to_point(0,0,0)
    draw_plane(@xmax_plane, [[x, bby1, bbz1],
                             [x, bby1, bbz2],
                             [x, bby2, bbz2], 
                             [x, bby2, bbz1]],3)

     x = @xmin_plane.distance_to_point(0,0,0)
     draw_plane(@xmin_plane, [[x, bby1, bbz1],
                              [x, bby1, bbz2],
                              [x, bby2, bbz2], 
                              [x, bby2, bbz1]],4)
  end

  if @options.show_yclip and @ymax_plane and @ymin_plane
    y = -1*@ymax_plane.distance_to_point(0,0,0)
    draw_plane(@ymax_plane, [[bbx1, y, bbz1],
                             [bbx1, y, bbz2],
                             [bbx2, y, bbz2], 
                             [bbx2, y, bbz1]],5)

     y = @ymin_plane.distance_to_point(0,0,0)
     draw_plane(@ymin_plane, [[bbx1, y, bbz1],
                              [bbx1, y, bbz2],
                              [bbx2, y, bbz2], 
                              [bbx2, y, bbz1]],6)
  end

end

#draw_init ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 520

def draw_init
  glClearColor(background.r,background.g,background.b,(@options.solid_bg ? 1.0 : 0.0))
  glEnable(GL_DEPTH_TEST)
  glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)


  # Antialiasing
  glEnable(GL_LINE_SMOOTH)
  glEnable(GL_BLEND)
  glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
  glHint(GL_LINE_SMOOTH_HINT, GL_NICEST)
  glHint(GL_POLYGON_SMOOTH_HINT, GL_NICEST)

  if @options.show_lighting
    glEnable(GL_LIGHTING)
    glEnable(GL_LIGHT0)
  else
    glDisable(GL_LIGHTING)
  end

  # Point size
  glPointSize(5)
  glLineWidth(2)
end

#draw_lattice(origin = [0,0,0]) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 760

def draw_lattice(origin = [0,0,0])

  return unless self.unit_cell
  
  atoms = if @options.correct
    @unit_cell.correct
  else
    @unit_cell
  end
  
  return unless atoms
  
  # Create sphere object
  rmin = 0.2
  rmax = 0.5

  if self.atoms_changed
    atoms.recache_visible_atoms 
    self.atoms_changed = false
  end
  
  # Calculate radius scaling factor vs. depth
  rrange = rmax - rmin
  # bb = atoms.bounding_box
  zmin = atoms.min{|a,b| a.z <=> b.z}.z
  zmax = atoms.max{|a,b| a.z <=> b.z}.z
  zrange = zmax - zmin
  if zrange == 0
    rscale = 0
  else
    rscale = rrange/zrange
  end



  sphere_quadric = nil
  for a in atoms
    a.material.apply(@options.show_lighting)
    case self.render_mode 
    when :ball_stick
      r = rmin+(a.z - zmin)*rscale
    else
      r = 2.0
    end
    
    sphere_quadric = draw_sphere(origin[0] + a.x, origin[1] + a.y, origin[2] + a.z, r, a.id, sphere_quadric)
    
  end
  gluDeleteQuadric(sphere_quadric) if sphere_quadric

end

#draw_plane(plane, lineLoop, pickid) ⇒ Object

Draw a plane use the vertices defined in lineLoop as the boundary of the plane



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# File 'lib/aims_project/crystal_viewer.rb', line 834

def draw_plane(plane, lineLoop, pickid)

  glPushName(pickid | PICK_ID_PLANE) if self.picking
  
  # if is_picked?(:plane, pickid)
  #   Material.black.apply
  #   glLineWidth(3.0)
  #   glEdgeFlag(GL_TRUE)
  # end
  glPolygonMode(GL_FRONT_AND_BACK, GL_FILL)

  Material.new(0.9, 0.9, 0.0, 0.5).apply
  glBegin(GL_TRIANGLE_FAN)
  glNormal3f(plane.a, plane.b, plane.c)
  lineLoop.each{|p| 
      glVertex3f(p[0], p[1], p[2])
  }
  glEnd()
  
  glEdgeFlag(GL_FALSE)
  glPopName() if picking
  
  if (is_picked?(:plane, pickid))
    Material.black.apply
    glLineWidth(3.0)
    glBegin(GL_LINE_LOOP)
    lineLoop.each{|p|
      glVertex3f(p[0], p[1], p[2])
    }
    glEnd()
    glLineWidth(1.0)
  end
  
end

#draw_scene ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 461

def draw_scene
  
  @glPanel.set_current
  sz = @glPanel.size
  viewport_setup(sz.width, sz.height)    
  
  
  begin
    draw_init
    apply_projection
    position_camera
    add_lights if @options.show_lighting
    outline_supercell if @options.show_supercell
    
    if self.unit_cell
      atoms = self.unit_cell
      @options.x_repeat.times do |i|
        @options.y_repeat.times do |j|
          @options.z_repeat.times do |k|
          
            origin = if self.unit_cell.lattice_vectors
              atoms.lattice_vectors[0]*i + atoms.lattice_vectors[1]*j + atoms.lattice_vectors[2]*k
            else
              Vector[0, 0, 0]
            end
            
            draw_bonds(origin) if @options.show_bonds
            draw_lattice(origin)
          end
        end
      end
    end
    draw_clip_planes
  rescue GeometryEvaluationException => e
  rescue AimsProjectException => e
    puts e.message
    puts e.backtrace.join("\n")
  end
  
  @glPanel.swap_buffers
end

#draw_sphere(x, y, z, r, name, sphere_quadric = nil) ⇒ Object

Draw an atom

Parameters:

  • x —

    The x-coordinate

  • y —

    The y-coordinate

  • z —

    The z-coordinate

  • r —

    The radius

  • name —

    The name of the sphere (for picking)

Returns:

  • a sphere_quadric for reuse if desired. Make sure to delete it when done



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# File 'lib/aims_project/crystal_viewer.rb', line 740

def draw_sphere(x,y,z,r, name, sphere_quadric=nil)

  unless sphere_quadric 
    sphere_quadric = gluNewQuadric()
    gluQuadricDrawStyle(sphere_quadric, GLU_FILL)
    gluQuadricNormals(sphere_quadric, GLU_SMOOTH)
    gluQuadricOrientation(sphere_quadric, GLU_OUTSIDE)
  end

  # Load a new matrix onto the stack
  glPushMatrix()
  glPushName(name | PICK_ID_ATOM) if self.picking
  glTranslatef(x, y, z)
  gluSphere(sphere_quadric, r, slices, stacks)            
  glPopName() if picking
  glPopMatrix()
  
  sphere_quadric
end

#dump_geometry ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 276

def dump_geometry
  atoms = self.unit_cell
  if atoms
    puts atoms.format_geometry_in
  end
end

#dump_properties ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 265

def dump_properties
  self.instance_variables.each{|v|
    puts "#{v} = #{self.instance_variable_get(v)}"
  }
end

#hiRes ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 443

def hiRes
  self.slices = 20
  self.stacks = 20
end

#image ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 949

def image
  image = Image.new(self.width, self.height)
  image.set_rgb_data(self.rgb_image_data)
  image.set_alpha_data(self.alpha_image_data)
	image
end

#init_clip_planes ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 226

def init_clip_planes
    
    # Thread.new(self) { |evtHandler|
      # @unit_cell_corrected = @unit_cell.correct
    #   evt = ThreadCallbackEvent.new
    #   evtHandler.add_pending_event(evt)
    # }
  
    return unless (@unit_cell and @unit_cell.is_valid?) 
  
    # each bounding box is a 2 element array [max, min]
    bounding_box = @unit_cell.bounding_box(false)
    xmax = bounding_box[0].x
    xmin = bounding_box[1].x
    ymax = bounding_box[0].y
    ymin = bounding_box[1].y
    zmax = bounding_box[0].z
    zmin = bounding_box[1].z

    @xmax_plane = Plane.new( 1, 0, 0, xmax, 0, 0)
    @xmin_plane = Plane.new(-1, 0, 0, xmin, 0, 0)
    @ymax_plane = Plane.new( 0, 1, 0, 0, ymax, 0)
    @ymin_plane = Plane.new( 0,-1, 0, 0, ymin, 0)
    @zmax_plane = Plane.new( 0, 0, 1, 0, 0, zmax)
    @zmin_plane = Plane.new( 0, 0,-1, 0, 0, zmin)

    # Add clip-planes to each unit cell
    @unit_cell.clear_planes
    @unit_cell.add_plane(@xmax_plane, false)
    @unit_cell.add_plane(@xmin_plane, false)
    @unit_cell.add_plane(@ymax_plane, false)
    @unit_cell.add_plane(@ymin_plane, false)
    @unit_cell.add_plane(@zmax_plane, false)
    @unit_cell.add_plane(@zmin_plane, false)
    @unit_cell.recache_visible_atoms
    @unit_cell.make_bonds(@options.bond_length)
  
end

#is_picked?(type, id) ⇒ Boolean

a test method to see of an object of a particular type was picked. valid types are :atom, :plane

Returns:

  • (Boolean) 


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# File 'lib/aims_project/crystal_viewer.rb', line 814

def is_picked?(type, id)
  if @picked
  case type
    when :atom
      @picked[:atoms].member? id
    when :plane
      @picked[:planes].member? id
    when :bond
      @picked[:bonds].member? id
    else
      false
    end
  else
    false
  end
end

#loRes ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 438

def loRes
  self.slices = 5
  self.stacks = 5
end

#mouse_down(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 289

def mouse_down(x,y)
  self.x_down = x
  self.y_down = y
  self.x_last = x
  self.y_last = y	  
  self.loRes
end

#mouse_dragged(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 337

def mouse_dragged(x, y)

  # Harmless correction for bug in WxRuby that doesn't register all mouse down events
  self.x_last = x if self.x_last.nil?
  self.y_last = y if self.y_last.nil? 
  self.z_last = z if self.z_last.nil?
  
  case self.mouse_motion_func
  when :rotate 
    rotate(x,y)
  when :zoom
    zoom(x,y)
  when :pan
    pan(x,y)
  when :move_clip_plane
    move_clip_plane(x,y)
  else
    rotate(x,y)
  end
  glutPostRedisplay if @using_glut
end

#mouse_up(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 297

def mouse_up(x,y)
  return unless self.unit_cell
  @picked = pick_object(x,y)
  self.atom = self.unit_cell.atoms.find{|a| a.id == @picked[:atoms].last}
  if self.atom
    @controller.select_atom(self.atom)
    # puts self.atom.format_geometry_in
  end
  
  unless @picked[:planes].empty?
    clip_plane_id = @picked[:planes].first
    @active_clip_plane = case clip_plane_id
    when 1 
      @zmax_plane
    when 2
      @zmin_plane
    when 3
      @xmax_plane
    when 4
      @xmin_plane
    when 5
      @ymax_plane
    when 6
      @ymin_plane
    else
      nil
    end
    if @active_clip_plane
      set_mouse_motion_function(:move_clip_plane)
    end
  end
  self.hiRes

  # Harmless correction for bug in WxRuby that doesn't register all mouse down events
  self.x_last = nil
  self.y_last = nil

  glutPostRedisplay if @using_glut
end

#move_clip_plane(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 386

def move_clip_plane(x,y)
  
  x_obj_last, y_obj_last, z_obj_last = unproject(x_last, y_last, 0)
  x_obj, y_obj, z_obj = unproject(x,y,0)

  w = [x_obj - x_obj_last, y_obj - y_obj_last, z_obj - z_obj_last]
  n = @active_clip_plane.unit_normal
  d = w[0]*n[0] + w[1]*n[1] + w[2]*n[2]
  
  # scale = 0.1
  # dx = (x - self.x_last)
  # dy = (y - self.y_last)
  # dr = sqrt(dx*dx + dy*dy)*(0 > dy ? -1 : 1)*scale
  self.x_last = x
  self.y_last = y

  @active_clip_plane.displace_along_normal(d)
  self.atoms_changed = true
end

#nudge(dir) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 197

def nudge(dir)
  @controller.nudge_selected_atoms(dir[0]*0.5, dir[1]*0.5, 0)
end

#outline_supercell ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 645

def outline_supercell
  return unless self.unit_cell
  uc = self.unit_cell

  vecs = uc.lattice_vectors
  return unless vecs

  origin = [0, 0, 0]
  v1 = vecs[0]
  v2 = vecs[1]
  v3 = vecs[2]

  # Corner #1
  c1 = v1 + v3

  # Corner #2
  c2 = v2 + v3

  # Corner #3
  c3 = v1 + v2

  # Corner #4
  c4 = v1 + v2 + v3

  Material.black.apply
  glLineWidth(1.0)

  glBegin(GL_LINES)

  glVertex3f(origin[0], origin[1], origin[2])
  glVertex3f(v1[0], v1[1], v1[2])				

  glVertex3f(origin[0], origin[1], origin[2])
  glVertex3f(v2[0], v2[1], v2[2])       

  glVertex3f(origin[0], origin[1], origin[2])
  glVertex3f(v3[0], v3[1], v3[2])       

  glVertex3f(v1[0], v1[1], v1[2])
  glVertex3f(c3[0], c3[1], c3[2])       

  glVertex3f(v2[0], v2[1], v2[2])
  glVertex3f(c3[0], c3[1], c3[2])       

  glVertex3f(c3[0], c3[1], c3[2])       
  glVertex3f(c4[0], c4[1], c4[2])       

  glVertex3f(v1[0], v1[1], v1[2])
  glVertex3f(c1[0], c1[1], c1[2])       

  glVertex3f(v2[0], v2[1], v2[2])
  glVertex3f(c2[0], c2[1], c2[2])       

  glVertex3f(c1[0], c1[1], c1[2])       
  glVertex3f(c4[0], c4[1], c4[2])       

  glVertex3f(c2[0], c2[1], c2[2])       
  glVertex3f(c4[0], c4[1], c4[2])       

  glVertex3f(v3[0], v3[1], v3[2])
  glVertex3f(c1[0], c1[1], c1[2])       

  glVertex3f(v3[0], v3[1], v3[2])
  glVertex3f(c2[0], c2[1], c2[2])       

  glEnd()        
end

#pan(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 423

def pan(x,y)
  
  z = 0.0 # This value is normalized with respect to the near and far clip planes

  obj_x, obj_y, obj_z = unproject(x, y, z)
  obj_x_last, obj_y_last, obj_z_last = unproject(x_last, y_last, z_last)
  @center.x += obj_x_last - obj_x
  @center.y += obj_y_last - obj_y
  @center.z += obj_z_last - obj_z
  
  self.x_last = x
  self.y_last = y
  self.z_last = z
end

#pick_object(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 545

def pick_object(x,y)

  buf = glSelectBuffer(512)
  glRenderMode(GL_SELECT)
  model = glGetDoublev(GL_MODELVIEW_MATRIX)
  proj = glGetDoublev(GL_PROJECTION_MATRIX)
  viewport = glGetIntegerv(GL_VIEWPORT);
  
  self.picking = true
  glMatrixMode(GL_PROJECTION)
  glLoadIdentity()
  gluPickMatrix(x,viewport[3]-y,5,5,viewport)
  if self.orthographic
    glOrtho(-self.ortho_side, self.ortho_side, -self.ortho_side,self.ortho_side, self.ortho_zmin, self.ortho_zmax)
  else
    gluPerspective(60, self.width/self.height, 1, 60)
  end
  
  z = 0.0 # This value is normalized with respect to the near and far clip planes
  obj_x, obj_y, obj_z = gluUnProject(x, viewport[3]-y, z, model, proj, viewport)
  
  glMatrixMode(GL_MODELVIEW)

  glInitNames
  if self.unit_cell 
    atoms = self.unit_cell
    @options.x_repeat.times do |i|
      @options.y_repeat.times do |j|
        @options.z_repeat.times do |k|
          
          # Hack to display non-periodic systems
          origin = if self.unit_cell.lattice_vectors
            atoms.lattice_vectors[0]*i + atoms.lattice_vectors[1]*j + atoms.lattice_vectors[2]*k
          else
            Vector[0,0,0]
          end
          
          self.draw_lattice(origin)
        end
      end
    end
  end
  self.draw_clip_planes

  self.picking = false

  glMatrixMode(GL_MODELVIEW);
  glFlush();

  count = glRenderMode(GL_RENDER)
  data = buf.unpack("L!*")
  names = []
  count.times do 
    num_names = data.shift
    min_depth = data.shift
    max_depth = data.shift
    num_names.times do 
      names << data.shift
    end
  end

  picked_objects = {:atoms => [], :planes => [], :bonds => []}
  names.each{|n|
    if (n & PICK_ID_ATOM) == PICK_ID_ATOM
      picked_objects[:atoms] << (n ^ PICK_ID_ATOM)
    end
    if (n & PICK_ID_PLANE) == PICK_ID_PLANE
      picked_objects[:planes] << (n ^ PICK_ID_PLANE)
    end
  }

  picked_objects
end

#position_camera ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 619

def position_camera
  return unless self.unit_cell
  atoms = self.unit_cell
  
  # Find the center of all atoms, not just visible ones.
  @center = atoms.center unless @center
  
  # Move camera out along z-axis
  glMatrixMode(GL_MODELVIEW)
  glLoadIdentity()

  glTranslatef(self.offx,self.offy,self.offz)
  glRotatef(self.alt, 1, 0, 0)
  glRotatef(self.az, 0, 0, 1)
  glTranslatef(-@center.x, -@center.y, -@center.z)
end

#rgb_image_data ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 956

def rgb_image_data

  # 3 bytes/pixel
  bytewidth = self.width*3
  bytes = bytewidth * self.height

  # Finish any pending Commands
  @glPanel.set_current
  glFinish

  # Setup pixel store
  glPixelStorei(Gl::GL_PACK_ALIGNMENT, 1) # Force byte alignment
  glPixelStorei(Gl::GL_PACK_ROW_LENGTH, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_ROWS, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_PIXELS, 0)

  glReadPixels(0, 0, self.width, self.height, Gl::GL_RGB, Gl::GL_UNSIGNED_BYTE)

end

#rgba_image_data ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 928

def rgba_image_data

  # 4 bytes/pixel
  bytewidth = self.width*4
  bytewidth = (bytewidth.to_i + 3) & ~3 # Align to 4 bytes
  bytes = bytewidth * self.height

  # Finish any pending Commands
  @glPanel.set_current
  glFinish

  # Setup pixel store
  glPixelStorei(Gl::GL_PACK_ALIGNMENT, 4) # Force 4-byte alignment
  glPixelStorei(Gl::GL_PACK_ROW_LENGTH, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_ROWS, 0)
  glPixelStorei(Gl::GL_PACK_SKIP_PIXELS, 0)

  glReadPixels(0, 0, self.width, self.height, Gl::GL_RGBA, Gl::GL_UNSIGNED_BYTE)

end

#rotate(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 406

def rotate(x,y)
  self.az += 5*(x - self.x_last)
  self.alt += 5*(y - self.y_last)
  self.x_last = x
  self.y_last = y
end

#set_defaults ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 158

def set_defaults
  self.current_cell = 0
  self.background = Material.new(0.7, 0.7, 1.0, 1)
  self.x_down = 0
  self.y_down = 0
  self.x_last = 0
  self.y_last = 0
  self.z_last = 0
  self.alt = 0
  self.az = 0
  self.offx = 0
  self.offy = 0
  self.offz = -20
  self.orthographic = true
  self.ortho_side = 15
  self.ortho_zmin = -1
  self.ortho_zmax = 50
  self.width = 500
  self.height = 500
  self.picking =false      
  # The last clicked atom
  self.atom = nil
  self.atoms_changed = true
  self.hiRes
  self.mouse_motion_func = :rotate
  self.repeat = Vector[1,1,1]
  self.render_mode = :ball_stick
  @options.set_properties(
    :bond_length => 3,
    :show_bonds => true,
    :show_lighting => true,
    :show_xclip => false,
    :show_yclip => false,
    :show_zclip => true,
    :show_supercell => true
  )
end

#set_mouse_motion_function(method_name) ⇒ Object

Executes the named method when the mouse is dragged



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# File 'lib/aims_project/crystal_viewer.rb', line 457

def set_mouse_motion_function(method_name)
  self.mouse_motion_func = method_name.to_sym
end

#set_view(offset_x, offset_y, offset_z, alt, az) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 448

def set_view(offset_x, offset_y, offset_z, alt, az)
  self.offx = offset_x
  self.offy = offset_y
  self.offz = offset_z
  self.alt = alt
  self.az = az
end

#unit_cell_changed ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 221

def unit_cell_changed
  init_clip_planes
  draw_scene
end

#unproject(x, y, z) ⇒ Object

Unproject the mouse coordinates to model space Handles the flipping of the y-coordinate



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# File 'lib/aims_project/crystal_viewer.rb', line 368

def unproject(x,y,z)
  model = glGetDoublev(GL_MODELVIEW_MATRIX)
  proj = glGetDoublev(GL_PROJECTION_MATRIX)
  viewport = glGetIntegerv(GL_VIEWPORT);

  gluUnProject(x, viewport[3]-y, z, model, proj, viewport)
end

#update ⇒ Object

Called when the options changes



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# File 'lib/aims_project/crystal_viewer.rb', line 154

def update
  self.draw_scene
end

#viewport_setup(width, height) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 503

def viewport_setup(width, height)
  self.width = width
  self.height = height
  glViewport(0, 0, self.width, self.height)
end

#zoom(x, y) ⇒ Object 



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# File 'lib/aims_project/crystal_viewer.rb', line 413

def zoom(x,y)
  if self.orthographic
    self.ortho_side -= (y - self.y_last)*0.1
  else
    self.offz -= (y - self.y_last)*0.1
  end
  self.x_last = x
  self.y_last = y
end