aims_project 0.3.0 → 0.3.1

data/bin/AimsProjectManager

@@ -14,6 +14,7 @@ require 'aims_project/atom.rb'
 require 'aims_project/inspector.rb'
 require 'aims_project/crystal_viewer.rb'
 require 'aims_project/geometry_editor.rb'
+require 'aims_project/geometry_console.rb'
 require 'aims_project/project_tree.rb'
 require 'aims_project/calculation_tree.rb'
 require 'aims_project/app_controller.rb'
@@ -25,15 +26,14 @@ require 'aims_project/crystal_viewer_options.rb'
 controller = AimsProject::AppController.new
 
 unless __FILE__.nil?
-  cwd = File.dirname(File.expand_path("."))
+  cwd = File.expand_path(".")
   controller.working_dir = cwd
 end
 
-controller.open_file(ARGV[0]) if ARGV[0]
 
-project_obj_files = Dir["*.yaml"]
-controller.project = AimsProject::Project.load(project_obj_files.first) unless project_obj_files.empty?
+# project_obj_files = Dir["*.yaml"]
+# controller.project = AimsProject::Project.load(project_obj_files.first) unless project_obj_files.empty?
 AimsProject::ThreadCallbackEvent.set_event_type(Wx::Event.new_event_type)
 Wx::EvtHandler.register_class(AimsProject::ThreadCallbackEvent, AimsProject::ThreadCallbackEvent.event_type, "evt_thread_callback", 0)
 
-controller.main_loop
+controller.main_loop

data/lib/aims_project/app_controller.rb

@@ -48,51 +48,13 @@ class AppController < Wx::App
         # Initialize the inspector
         @inspector = Inspector.new(self, @frame)
         
-        # Create the notebook
-        @notebook = Notebook.new(@frame)
-        
         # Create the geometry notebook page
-        @geomWindow = GeometryWindow.new(self, @notebook)
-
-        # Create the control window
-        # The base window is a horizontal splitter
-        # Left side is a list of control files
-        # right side is a Rich Text Control
-        controlWindow = SplitterWindow.new(@notebook)
-        @controlList = ListCtrl.new(controlWindow);
-        @controlEditor = RichTextCtrl.new(controlWindow)
-        controlWindow.split_horizontally(@controlList, @controlEditor)
-        
-        # Create the calculations window
-        # Similar to the geometryWindow
-        # Left side is a list control
-        # Right side is a crystal viewer
-        calcWindow = CalculationWindow.new(self, @notebook)
-        
-        # Add windows to the notebook
-        @notebook.add_page(@geomWindow, 'Geometry')
-        @notebook.add_page(controlWindow, "Control")
-        @notebook.add_page(calcWindow, "Calculations")
-        
-        evt_notebook_page_changed(@notebook) {|evt|
-          cp = @notebook.get_current_page
-          if cp.respond_to? :show_inspector
-            @notebook.get_current_page.show_inspector
-          end
-        }
-        
-        # Set the selected notebook page
-        @notebook.set_selection(2)
-        
-        # @tree = ProjectTree.new(self, hsplitter)
+        @geomWindow = GeometryWindow.new(self, @frame)
+        frameSizer = VBoxSizer.new
+        # frameSizer.add_item(@geomWindow, :proportion => 1, :flag => EXPAND)
+        #         @frame.set_sizer(frameSizer)
         @frame.set_menu_bar(menubar)
-        # @toolbar = @frame.create_tool_bar
-        # populate_toolbar(@toolbar) if @toolbar
-                
 
-        # Check off the current tool
-        # set_tool
-        
         # Display
         @frame.show        
    end
@@ -172,6 +134,7 @@ class AppController < Wx::App
    
    # Show the inspector
    def show_inspector
+     @geomWindow.show_inspector
      @inspector.show(true)
    end
    
@@ -208,18 +171,9 @@ class AppController < Wx::App
          end
        end
        puts "Opening #{file}"
-
+       @geomWindow.open_geometry_file(file)
        @frame.set_title(file)
-       @geomEditor.show
-       @calcTree.hide
-       
-       if (project)
-         erb = ERB.new(File.read(file))
-         show_geometry Aims::GeometryParser.parse_string(erb.result(project.get_binding))
-       else
-         show_geometry Aims::GeometryParser.parse(file)
-       end
-       
+         
        
      rescue Exception => dang
        error_dialog(dang)
@@ -228,37 +182,35 @@ class AppController < Wx::App
    alias_method :open_file, :open_geometry_file
    
    def save_geometry
-     page = @notebook.get_current_page
-     if (page.respond_to? :geometry)  && not(page.geometry.nil?)
-       geometry = @notebook.get_current_page.geometry
-       begin
+     geometry = @geomWindow.geometry
+     begin
+       if geometry.file
          geometry.save
-       rescue Exception => e
-         error_dialog(e)
+       else
+         save_geometry_as
        end
-     end     
+     rescue Exception => e
+       error_dialog(e)
+     end
    end
    
    # Save the geometry
    def save_geometry_as
      
-     page = @notebook.get_current_page
-     if (page.respond_to? :geometry)  && not(page.geometry.nil?)
-       geometry = @notebook.get_current_page.geometry
+       geometry = @geomWindow.geometry
        
-       fd = TextEntryDialog.new(@frame, :message => "Save Geometry", :caption => "Specify name of geometry:")
+       fd = FileDialog.new(@frame, :message => "Save Geometry", :style => FD_SAVE, :default_dir => @working_dir)
        if Wx::ID_OK == fd.show_modal
          begin
-           geom_name = fd.get_value
-           new_geom  = geometry.save_as(File.new(File.join(GEOMETRY_DIR, geom_name), "w"))
-           @geomWindow.add_geometry(new_geom)
+           @working_dir = fd.get_directory
+           geom_name = fd.get_path
+           new_geom  = geometry.save_as(geom_name)
+           @geomWindow.show_geometry(new_geom)
          rescue Exception => e
            error_dialog(e)
          end
        end 
-     else
-       error_dialog("No geometry selected.")
-     end
+
    end
 
    # Display an error dialog for the exception
@@ -275,19 +227,14 @@ class AppController < Wx::App
    def save_image
 
      begin
-       page = @notebook.get_current_page
-       if (page.respond_to? :image) 
-         image = page.image
+         image = @geomWindow.image
          fd = FileDialog.new(@frame, :message => "Save Image", :style => FD_SAVE, :default_dir => @working_dir)
          if Wx::ID_OK == fd.show_modal
            @working_dir = fd.get_directory
             puts "Writing #{fd.get_path}"
             image.mirror(false).save_file(fd.get_path)
           end
-       else
-         error_dialog("Sorry, could not generate an image.")
-       end
-
+       
       rescue Exception => e
         error_dialog(e)
       end

data/lib/aims_project/crystal_viewer.rb

@@ -214,7 +214,8 @@ class CrystalViewer < Wx::Panel
     init_clip_planes
     
     @unit_cell.add_observer(self, :unit_cell_changed)
-
+    draw_scene
+    
   end
 
   def unit_cell_changed
@@ -223,13 +224,15 @@ class CrystalViewer < Wx::Panel
   end
 
   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
@@ -475,8 +478,12 @@ class CrystalViewer < Wx::Panel
           @options.y_repeat.times do |j|
             @options.z_repeat.times do |k|
             
-              origin = atoms.lattice_vectors[0]*i + atoms.lattice_vectors[1]*j + atoms.lattice_vectors[2]*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
@@ -484,6 +491,7 @@ class CrystalViewer < Wx::Panel
         end
       end
       draw_clip_planes
+    rescue GeometryEvaluationException => e
     rescue AimsProjectException => e
       puts e.message
       puts e.backtrace.join("\n")
@@ -558,20 +566,25 @@ class CrystalViewer < Wx::Panel
     glMatrixMode(GL_MODELVIEW)
 
     glInitNames
-    if self.unit_cell
+    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 = atoms.lattice_vectors[0]*i + atoms.lattice_vectors[1]*j + atoms.lattice_vectors[2]*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)
-            self.draw_clip_planes
           end
         end
       end
     end
+    self.draw_clip_planes
 
     self.picking = false
 
@@ -609,7 +622,7 @@ class CrystalViewer < Wx::Panel
     
     # 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()

data/lib/aims_project/geometry_console.rb

@@ -0,0 +1,155 @@
+
+module AimsProject
+  
+  class CommandHistory
+
+    def initialize
+      @history= []
+      @counter = 0
+    end
+
+    def save(cmd)
+      @history.push(cmd)
+      @counter = @history.size
+    end
+    
+    def prev
+      @counter = @history.size unless @counter
+      if @counter > 0
+        @counter = @counter - 1
+      end
+      @history[@counter]
+    end
+    
+    def succ
+      @counter = @history.size unless @counter
+      if @counter < @history.size-1
+        @counter = @counter + 1
+      end
+      @history[@counter]
+    end
+  end
+  
+  class GeometryConsole < Wx::ScrolledWindow
+    
+    include Wx
+    include Aims
+    
+    def initialize(app, window)
+      super(window)
+      @app = app
+      @text_ctrl = RichTextCtrl.new(self)
+      @history = CommandHistory.new
+      sizer = BoxSizer.new(VERTICAL)
+      sizer.add_item(@text_ctrl, :proportion => 1, :flag => EXPAND | ALL, :border => 5)
+
+      set_auto_layout(true)
+      set_sizer(sizer)
+      prompt
+      
+      @text_ctrl.evt_key_down do |evt|
+        k = evt.get_key_code
+        caret_pos = @text_ctrl.get_insertion_point
+        
+        case k
+        when K_UP
+          prev = @history.prev
+          @text_ctrl.remove(@line_start, @text_ctrl.get_last_position)
+          @text_ctrl.append_text(prev) if prev
+        when K_DOWN
+          succ = @history.succ
+          @text_ctrl.remove(@line_start,@text_ctrl.get_last_position)
+          @text_ctrl.append_text(succ) if succ
+        when K_LEFT
+          if caret_pos > @line_start
+            @text_ctrl.set_insertion_point(caret_pos-1)
+          end
+        when K_RIGHT
+          if caret_pos < @text_ctrl.get_last_position
+            @text_ctrl.set_insertion_point(caret_pos+1)
+          end          
+        else
+          if caret_pos < @line_start
+            @text_ctrl.set_insertion_point(@line_start+1)
+          end
+          evt.skip
+        end
+      end
+      
+      @text_ctrl.evt_char do |evt|
+        k = evt.get_key_code
+        case k
+        when K_RETURN
+          cmd = @text_ctrl.get_range(@line_start, @text_ctrl.get_caret_position+1).strip
+          @history.save(cmd)
+          print "\n"
+          # evaluate
+          begin
+            result = get_binding.eval(cmd)
+            if result
+              result_str = result.to_s
+              print(result_str+"\n") 
+            end
+          rescue Exception => e
+            print(e.message + "\n", Wx::RED)
+          end
+
+          prompt
+        when K_HOME # For some reason, ctrl-a maps to this
+          @text_ctrl.set_insertion_point(@line_start)
+        when K_HELP # For some reason, ctrl-e maps to this
+          @text_ctrl.set_insertion_point_end
+        else
+          evt.skip()
+        end
+      end
+      
+    end
+    
+    def get_binding
+      unless @binding
+        @binding = binding()
+      end
+      @binding
+    end
+    
+    def prompt
+      @text_ctrl.append_text(">> ")
+      @text_ctrl.move_end
+      @line_start = @text_ctrl.get_caret_position + 1
+      @text_ctrl.show_position(@line_start)
+    end
+    
+    def print(str, color=Wx::BLACK)
+      start = @text_ctrl.get_caret_position
+      @text_ctrl.append_text(str)
+      stop = @text_ctrl.get_caret_position
+      @text_ctrl.set_style(start..stop, RichTextAttr.new(color))
+    end
+    
+    def echo(str, color=Wx::BLACK)
+      print(str+"\n", color)
+      return nil
+    end
+    
+    def ls(pattern = "*")
+      match = Dir[pattern]
+      print(match.join("\n") + "\n")
+      return nil
+    end
+    
+    def geometry
+      @app.geometry
+    end
+    
+    def set_geometry(geom)
+      if geom.is_a? Aims::Geometry
+        puts "All Good"
+        @app.show_geometry(GeometryFile.new(geom))
+      else
+        echo("Not a valid geometry object")
+      end
+    end
+    
+  end
+end

data/lib/aims_project/geometry_editor.rb

@@ -21,37 +21,18 @@ class GeometryEditor < Wx::ScrolledWindow
     # Create the button panel (A toolbar for the top of this panel)
     @button_panel = HBoxSizer.new
     
-    @toggle_source = CheckBox.new(self, ID_ANY, "Source")
-    
     basedir = File.dirname(__FILE__)
     arrow_icon = Image.new(File.join(basedir,"green_arrow.jpg"), BITMAP_TYPE_JPEG)
     @eval_button = BitmapButton.new(self, :bitmap => arrow_icon.rescale(16,15).convert_to_bitmap,:style=>BU_EXACTFIT, :name => "evaluate")
     
-    # error_icon = Image.new(File.join(basedir, "red_cross.jpeg"), BITMAP_TYPE_JPEG)
-    # @clear_errors_button = BitmapButton.new(self, :bitmap => error_icon.rescale(16,15).convert_to_bitmap,:style=>BU_EXACTFIT, :name => "Clear Errors")
-    
-    @button_panel.add_item(@toggle_source,1)
-    @button_panel.add_stretch_spacer
     @button_panel.add_item(@eval_button,3)
-    
-    evt_checkbox(@toggle_source) {|evt|
-      if @toggle_source.is_checked
-        @text_ctrl.set_read_only(false)
-        @text_ctrl.set_text(@unit_cell.raw_input)
-      else
-        @text_ctrl.set_read_only(false)
-        @text_ctrl.set_text(@unit_cell.input_geometry)
-        @text_ctrl.set_read_only(true)
-      end
-    }
-    
+        
     sizer.add_item(@button_panel, :flag => EXPAND)
     sizer.add_item(@text_ctrl, :proportion => 1, :flag => EXPAND | ALL, :border => 5)
 
     set_auto_layout(true)
     set_sizer(sizer)
-
-        
+    
     evt_button(@eval_button) {|event|
         self.evaluate
     }
@@ -60,28 +41,19 @@ class GeometryEditor < Wx::ScrolledWindow
   
   # Apply the edits to the geometry_file and evaluate
   def evaluate
+    
     @unit_cell.raw_input = @text_ctrl.get_text
     begin
       @unit_cell.evaluate    
     rescue 
       # @button_pane.add_item(@clear_errors_button, 3)
-      @text_ctrl.set_text($!.message + $!.backtrace.join("\n"))
+      @app.display_exception($!)
     end
   end
   
   def unit_cell=(uc)
     @unit_cell = uc
-    if @toggle_source.is_checked
-      @text_ctrl.set_read_only(false)
-      @text_ctrl.set_text(@unit_cell.raw_input)
-      @text_ctrl.set_read_only(false)
-      
-    else
-      @text_ctrl.set_read_only(false)
-      @text_ctrl.set_text(@unit_cell.input_geometry)
-      @text_ctrl.set_read_only(true)
-      
-    end
+    @text_ctrl.set_text(@unit_cell.input_geometry)      
   end
   
   def select_atom(atom)

data/lib/aims_project/geometry_file.rb

@@ -43,7 +43,13 @@ module AimsProject
     # @param input If input is a File, the file is read and evaluated with ERB
     #             If input is a String, the input is directly evaluated with ERB
     # @param _binding The binding to use when evaluating with EB
-    def initialize(input, _binding=nil)
+    def initialize(input = nil, _binding=nil)
+      
+      if input.nil?
+        @raw_input = ""
+        @input_geometry = ""
+        return
+      end
       
       if input.respond_to? :read
         @file = input
@@ -67,12 +73,8 @@ module AimsProject
     # Set the raw input
     # @param str The string to set the raw input to
     # @param notify Whether or not to notify observer. Set this to false if you intend to call evaluate immediately after
-    def raw_input=(str, notify = true)
+    def raw_input=(str)
       @raw_input = str
-      if notify
-        changed
-        notify_observers
-      end
     end
     
     # Evaluate the raw input and return a geometry String formatted in the Aims geometry.in format
@@ -91,6 +93,7 @@ module AimsProject
       @aims_geometry
     end
     
+    
     # Delegate calls to the Aims::Geometry object if it exists.
     def method_missing(symbol, *args, &block)
       if @aims_geometry.nil?
@@ -105,7 +108,7 @@ module AimsProject
       begin
         validate
         return true
-      rescue GeometryValidationException => e
+      rescue Exception => e
         return false
       end
     end
@@ -170,11 +173,7 @@ module AimsProject
           f.write @raw_input
         }
         
-        if file == @file
-          return self
-        else
-          GeometryFile.new(File.new(file.path, "r"))
-        end
+        return self
         
     end
     

data/lib/aims_project/geometry_window.rb

@@ -29,15 +29,7 @@ module AimsProject
       sizer.add_item(topSplitterWindow, :proportion => 1, :flag => EXPAND)
       
       set_sizer(sizer)
-      
-      # The top is a list control
-      @geomList = ListCtrl.new(topSplitterWindow)
-      app.project.geometries.sort{|a,b| a <=> b}.each{|geom|
-        li = ListItem.new
-        li.set_text(File.basename(geom))
-        li.set_data(geom)
-        @geomList.insert_item(li)
-      }
+      @console = GeometryConsole.new(self, topSplitterWindow)
       
       # The bottom is a vertical splitter
       geomWindowSplitter = SplitterWindow.new(topSplitterWindow)
@@ -47,26 +39,17 @@ module AimsProject
       geomWindowSplitter.split_vertically(@geomEditor, @geomViewer)
       
       # Add top and bottom sides together
-      topSplitterWindow.split_horizontally(@geomList, geomWindowSplitter, 100)
+      topSplitterWindow.split_horizontally(geomWindowSplitter, @console, -100)
       layout
       
       # Define events
-      evt_list_item_selected(@geomList) {|evt|
+      evt_list_item_selected(@console) {|evt|
         open_geometry_file(evt.get_item.get_data)
       }
       
+      show_geometry(GeometryFile.new)
+      
       
-    end
-    
-    # Add a geometry with the given name
-    def add_geometry(geometry)
-      @app.project.geometries << geometry
-      li = ListItem.new
-      li.set_text(File.basename(geometry.file))
-      li.set_data(geometry.file)
-      li.set_state(LIST_STATE_SELECTED)
-      @geomList.insert_item(li)
-      @geomList.sort{|a,b| a <=> b}
     end
     
 
@@ -114,7 +97,7 @@ module AimsProject
       begin
         @original_uc = geometry
         @geomViewer.unit_cell = @original_uc
-      rescue AimsProjectException => e
+       rescue AimsProjectException => e
         @app.error_dialog(e)
       ensure
         @geomEditor.unit_cell = @original_uc
@@ -128,6 +111,7 @@ module AimsProject
       puts "Selection:" 
       puts @selection[:atoms].each{|a| puts a.format_geometry_in}
       @geomEditor.select_atom(atom)
+      @console.echo(atom.to_s)
     end
     
     def nudge_selected_atoms(x,y,z)
@@ -138,6 +122,10 @@ module AimsProject
       @geomEditor.update
     end
     
+    def display_exception(e)
+      @console.print(e.message, Wx::RED)
+    end
+    
     # Apply UI settings to viewer and re-render
     def update_viewer
       

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: aims_project
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,22 +9,22 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-22 00:00:00.000000000Z
+date: 2013-05-30 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: wxruby-ruby19
-  requirement: &5405190 !ruby/object:Gem::Requirement
+  requirement: &5564000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.0.1
+        version: 2.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *5405190
+  version_requirements: *5564000
 - !ruby/object:Gem::Dependency
   name: ruby-opengl2
-  requirement: &5404960 !ruby/object:Gem::Requirement
+  requirement: &5563770 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 0.60.3
   type: :runtime
   prerelease: false
-  version_requirements: *5404960
+  version_requirements: *5563770
 - !ruby/object:Gem::Dependency
   name: aims
-  requirement: &5404730 !ruby/object:Gem::Requirement
+  requirement: &5563540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 0.3.0
   type: :runtime
   prerelease: false
-  version_requirements: *5404730
+  version_requirements: *5563540
 - !ruby/object:Gem::Dependency
   name: highline
-  requirement: &5404500 !ruby/object:Gem::Requirement
+  requirement: &5563310 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.6.11
   type: :runtime
   prerelease: false
-  version_requirements: *5404500
+  version_requirements: *5563310
 - !ruby/object:Gem::Dependency
   name: capistrano
-  requirement: &5404270 !ruby/object:Gem::Requirement
+  requirement: &5563080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,7 +65,7 @@ dependencies:
         version: 2.11.2
   type: :runtime
   prerelease: false
-  version_requirements: *5404270
+  version_requirements: *5563080
 description: This gem simplifies and streamlines the calculation pipeline for FHI-AIMS.
 email: joshua.shapiro@gmail.com
 executables:
@@ -84,6 +84,7 @@ files:
 - lib/aims_project/calculation_window.rb
 - lib/aims_project/crystal_viewer.rb
 - lib/aims_project/crystal_viewer_options.rb
+- lib/aims_project/geometry_console.rb
 - lib/aims_project/geometry_editor.rb
 - lib/aims_project/geometry_file.rb
 - lib/aims_project/geometry_window.rb
@@ -108,7 +109,7 @@ files:
 - bin/AimsProjectManager
 - bin/AimsCalc
 - bin/AimsProject
-homepage: 
+homepage: https://github.com/jns/AimsProject
 licenses: []
 post_install_message: 
 rdoc_options: []