aims_project 0.3.0

data/bin/AimsProjectManager

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+#!/usr/bin/env ruby
+
+require "rubygems"
+
+require "wx"
+require "erb"
+require "gl"
+require "glu"
+
+require 'aims'
+require 'aims_project'
+require 'aims_project/material.rb'
+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/project_tree.rb'
+require 'aims_project/calculation_tree.rb'
+require 'aims_project/app_controller.rb'
+require 'aims_project/geometry_window.rb'
+require 'aims_project/calculation_window.rb'
+require 'aims_project/thread_callback_event.rb'
+require 'aims_project/crystal_viewer_options.rb'
+
+controller = AimsProject::AppController.new
+
+unless __FILE__.nil?
+  cwd = File.dirname(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?
+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

data/lib/aims_project.rb

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+
+# AimsProject is an application for visualizing and managing projects for
+# the FHI-AIMS package
+
+require "rubygems"
+require 'aims'
+require 'yaml'
+
+require 'aims_project/project.rb'
+require 'aims_project/calculation.rb'
+require 'aims_project/geometry_file.rb'
+require 'aims_project/aims_project_exception.rb'
+
+# AimsProject is a set of tools for managing and organizing 
+# calculations for executaion on high-performance computing clusters.
+# It is designed specifically for the FHI-AIMS package published
+# by the Fritz-Haber Institute (https://aimsclub.fhi-berlin.mpg.de), 
+# but can probably be generatlized to other codes.
+#
+# Author: Joshua Shapiro (email:joshua.shapiro@gmail.com)
+# Copyright: 2012 Joshua Shapiro
+# License: TBD
+#
+# = Why should I use AimsProject?
+# Good organization is crucial to obtaining meaningful results with
+# the FHI-AIMS package.  Careful testing of convergence 
+# across parameters in the control and geometry files easily requires
+# dozens of calculations.  The novice and expert user alike can quickly 
+# lose track of which calculations are complete, which are still pending,
+# which calculations were errors, and which calculations failed or were aborted.
+# In this framework, even the most experienced user can and will make mistakes.  
+#
+# <em>The aim of this tool is to simplify and streamline the calculation 
+# pipeline, so the user can focus on the results.</em>
+# 
+# = Features
+# * Automated generation of calculations from control & geometry files.
+# * Automated synchronization between a workstation and the compute cluster. 
+# * Automated job submission of pending calculations to the queue
+# * Status tracking of calculations from creation to completion.
+# * Simple organizational structure with human readable metadata. 
+#   
+# = Planned Features
+# * Input file validation (To catch mistakes before submitting to a queue)
+# * Geometry input and output visualization
+# 
+# = Quick Start
+# == Installation
+#
+#    gem install aims_project
+#
+# == Creating a Project
+#
+# Type:
+#       AimsProject myProject
+# 
+# This will create the directory structure
+#      myProject
+#       -> calculations/
+#       -> config/
+#       -> control/
+#       -> geometry/
+#       -> Capfile
+#       -> myProject.yaml
+#
+# 
+# +calculations+:: Contains one subdirectory for each calculation.
+# +config+:: Contains special configuration files for automation.
+# +geometry+:: This is where you will place all your geometry files.
+# +control+:: This is where you place all your control files.
+# +Capfile+:: Location where you customize the interaction with the compute cluster
+# +myProject.yaml+:: Human readable metadata related to this project.
+#
+# == Creating a calculation
+#
+# Assume you are investigating two atomic configurations _alpha_ and _beta_, and
+# you want to calculate them with the _light_ and _tight_ settings. 
+# 
+# Create the FHI-AIMS formatted input files and name them 
+# * +geometry/alpha+
+# * +geometry/beta+
+# * +control/light+
+# * +control/tight+
+#
+# Now run 
+#    > AimsCalc create alpha light
+#    > AimsCalc create beta light
+#    > AimsCalc create alpha tight
+#    > AimsCalc create beta tight
+#
+# This will create four subdirectories inside +calculations/+.
+#    > ls calculations/*
+#     calculations/alpha.light:
+#     calc_status.yaml   control.in       geometry.in
+#     
+#     calculations/alpha.tight:
+#     calc_status.yaml   control.in       geometry.in
+#     
+#     calculations/beta.light:
+#     calc_status.yaml   control.in       geometry.in
+#     
+#     calculations/beta.tight:
+#     calc_status.yaml   control.in       geometry.in
+#     
+# Notice that each calculation directory has the required +control.in+ and 
+# +geometry.in+ file.  These were directly copied from the geometry and control files
+# passed to AimsCalc.  *Note* It is possible to embed variables inside the control
+# and geometry files, see AimsCalc for more details. Each directory also contains
+# a file named +calc_status.yaml+.  This is a metadata file used for tracking
+# the history and status of the calculation.  Currently this file looks something like
+#    --- !ruby/object:AimsProject::Calculation 
+#    control: light
+#    geometry: alpha
+#    status: STAGED
+# 
+# 
+# Feel free to get more creative with the geometry and control file names.  You should encode
+# as much information in the file name as possible, as this will make it easy 
+# for you to identify the calculation later.  For example, a geometry file 
+# named +alpha2x2_5layers_relaxed+ and a control file named +light_tier1_norelax_6x6x1_lomem+
+# will result in a calulation directory named +alpha2x2_5layers_relaxed.light_tier1_norelax_6x6x1_lomem+
+#
+# == Running a Calculation
+# At this point the calculation status is +STAGED+.  To run the calculation, first customize
+# the +Capfile+ with details necessary for running FHI-AIMS on the computing cluster. 
+# Check this file carefully, this is where you define the name and location of the aims executable, 
+# the name of the server, and the method for submitting jobs to the queue.  Once this file 
+# is properly configured, the calculations are submitted with one line:
+# 
+#     cap aims:enqueue
+#
+# This command invokes custom tasks in +Capistrano+, a 3rd party tool for automated deployment, 
+# that will upload the calculations to the server and submit them to the queue.
+# 
+
+
+
+module AimsProject
+  # Constants
+  STAGED   = "STAGED"
+  HOLD     = "HOLD"
+  QUEUED   = "QUEUED"
+  RUNNING  = "RUNNING"
+  COMPLETE = "COMPLETE"
+  ABORTED  = "ABORTED"
+  CANCELED = "CANCELED"
+  
+  CONFIG_DIR = "config"
+  CALCULATION_DIR = "calculations"
+  GEOMETRY_DIR = "geometry"
+  CONTROL_DIR = "control"
+  CALC_STATUS_FILENAME = "calc_status.yaml"
+  PROJECT_VARIABLES_FILENAME = "project_vars.rb"
+  
+  GLOBAL_CONFIG_DIR = File.join(ENV["HOME"], ".aims_project")
+  GLOBAL_VARIABLES_FILENAME = "aims_project_vars.rb"
+
+end

data/lib/aims_project/aims_project_exception.rb

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+
+module AimsProject
+  class AimsProjectException < StandardError
+  end
+
+  class InvalidFilenameException < AimsProjectException
+    def initialize(filename)
+      if filename.nil?
+        super "No filename specified"
+      else
+        super "The filename #{filename} is invalid."
+      end
+    end
+  end
+  
+  class ObjectFileNotFoundException < AimsProjectException
+    def initialize(filename)
+      super "The serialized yaml file was not found: #{filename}"
+    end
+  end
+  
+  class CorruptObjectFileException < AimsProjectException
+    def initialize(filename)
+      super "The serialized yaml file is corrupt: #{filename}"
+    end
+  end
+  
+  class GeometryValidationException < AimsProjectException
+    attr_reader :violations
+    def initialize(violations)
+      @violations = violations
+      super "The Geometry failed validation."
+    end
+  end
+  
+  class GeometryEvaluationException < AimsProjectException
+    def initialize
+      super "Error evaluating geometry"
+    end
+  end
+  
+end

data/lib/aims_project/aims_project_geometry.rb

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+module AimsProject
+  
+  # A class that encapsulates the Aims::Geometry and other
+  # state information important for AimsProject
+  class AimsProjectGeometry
+    
+    # Boolean flag indicating whether the atoms should be displaced to all lie
+    # within the unit cell
+    attr_accessor :correct_geometry
+
+    # The filename defining this geometry
+    attr_reader :filename
+    
+    def initialize(file)
+      @filename = file
+      @geometry_original = Aims::GeometryParser.parse(@filename)
+    end
+    
+    def geometry
+      if self.correct_geometry
+        geometry_corrected
+      else
+        geometry_original
+      end
+    end
+    
+    def geometry_corrected
+      if @geometry_corrected.nil?
+        @geometry_corrected = @geometry_original.correct
+      end
+      @geometry_corrected
+    end
+    
+    def geometry_original
+      @geometry_original
+    end
+    
+    def to_s
+      @filename
+    end
+    
+    
+    def save
+      unless @filename
+        raise InvalidFilenameException
+      end
+      raise "AimsProjectGeometry.save is not yet implemented"
+    end
+    
+  end
+  
+end

data/lib/aims_project/app_controller.rb

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+
+module AimsProject
+class AppController < Wx::App
+  
+    include Wx
+  
+    ID_NEW = 102
+    ID_SAVE_IMAGE = 103  
+    ID_MOVE_CLIP_PLANE = 104
+    ID_SAVE_AS = 105
+
+    ID_INSPECTOR = 201
+
+    ID_DELETE_ATOM = 301
+    
+    @frame = nil
+    @menubar = nil
+    @inspector = nil
+    @statusbar = nil
+
+    # The project
+    attr_accessor :project
+    
+    # Used to synchronize directory in open/save dialogs
+    attr_accessor :working_dir
+    
+    # The root frame
+    attr_accessor :frame
+    
+   # Build the application
+   def on_init
+     
+        self.app_name = "AimsViewer"
+        # Create the frame, toolbar and menubar and define event handlers
+        size = [1000,700]
+        @frame = Frame.new(nil, -1, "AimsViewer", DEFAULT_POSITION, size)
+        @statusbar = @frame.create_status_bar
+
+        # This timer will cause the main thread to pass every 2 ms so that other threads
+        # can get work done.
+        timer = Wx::Timer.new(self, Wx::ID_ANY)
+        evt_timer(timer.id) {Thread.pass}
+        timer.start(2)
+
+        # Initialize the selection
+        @selection = {}
+        
+        # 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)
+        @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
+   
+   # Process a menu event
+   def process_menu_event(event)
+     case event.id
+     when ID_INSPECTOR
+       show_inspector
+     when ID_DELETE_ATOM
+       delete_atom
+     when Wx::ID_OPEN
+       open_file
+     when Wx::ID_SAVE
+       save_geometry
+     when ID_NEW
+       new_geometry_file
+     when ID_SAVE_AS
+       save_geometry_as
+     when ID_SAVE_IMAGE
+       save_image
+     when Wx::ID_EXIT
+        exit(0)
+     else
+       event.skip
+     end
+     
+   end
+
+   
+   # Return the menubar.  If it is undefined, then define it and attach the event handler
+   def menubar
+     unless @menubar
+       fileMenu = Menu.new
+       fileMenu.append(ID_NEW, "New Geometry ...")
+       fileMenu.append(Wx::ID_OPEN, "Open ...\tCTRL+o")
+       fileMenu.append(Wx::ID_SAVE, "Save Geometry\tCTRL+s")
+       fileMenu.append(ID_SAVE_AS, "Save Geometry As...")
+       fileMenu.append(ID_SAVE_IMAGE, "Export Image ...")
+       fileMenu.append(Wx::ID_EXIT, "Exit")
+       
+       editMenu = Menu.new
+       editMenu.append(ID_DELETE_ATOM, "Delete Atom\tCTRL+d")
+       
+       toolsMenu = Menu.new       
+       # toolsMenu.append(ID_ROTATE, "rotate", "Rotate", Wx::ITEM_CHECK)
+       # toolsMenu.append(ID_ZOOM, "zoom", "Zoom", Wx::ITEM_CHECK)
+       # toolsMenu.append(ID_PAN, "pan", "Pan", Wx::ITEM_CHECK)
+       # toolsMenu.append(ID_MOVE_CLIP_PLANE, "move cilp plane", "Move", Wx::ITEM_CHECK)
+       
+       viewMenu = Menu.new
+       viewMenu.append(ID_INSPECTOR, "inspector\tCTRL+i")
+       
+       
+       @menubar = MenuBar.new
+       @menubar.append(fileMenu, "File")
+       @menubar.append(editMenu, "Edit")
+       @menubar.append(viewMenu, "Views")
+       @menubar.append(toolsMenu, "Tools")
+       
+       evt_menu @menubar, :process_menu_event
+     end
+     @menubar
+   end
+   
+   def set_status(string)
+     @frame.set_status_text(string)
+   end
+   
+   # Get the inspector
+   def inspector
+     if @inspector.nil?
+       @inspector = Inspector.new(self, @frame)
+     end
+     @inspector
+   end
+   
+   # Show the inspector
+   def show_inspector
+     @inspector.show(true)
+   end
+   
+   # Hide the inspector
+   def hide_inspector
+     @inspector.hide
+   end
+   
+   # Create a new geometry file
+   def new_geometry_file(file = nil)
+     fd = TextEntryDialog.new(@frame, :message => "New Geometry", :caption => "Specify name of geometry:")
+      if Wx::ID_OK == fd.show_modal
+        begin
+          geom_name = fd.get_value
+          geometry = GeometryFile.new("")
+          geometry = geometry.save_as(File.new(File.join(GEOMETRY_DIR, geom_name), "w"))
+          @geomWindow.add_geometry(geometry)
+        rescue Exception => e
+          error_dialog(e)
+        end
+      end
+   end
+   
+   # Display a file dialog and attempt to open and display the file
+   def open_geometry_file(file = nil)
+     begin
+       unless file
+         fd = FileDialog.new(@frame, :message => "Open", :style => FD_OPEN, :default_dir => @working_dir)
+         if ID_OK == fd.show_modal
+           file = fd.get_path
+           @working_dir = fd.get_directory
+         else
+           return
+         end
+       end
+       puts "Opening #{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)
+     end
+   end
+   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.save
+       rescue Exception => e
+         error_dialog(e)
+       end
+     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
+       
+       fd = TextEntryDialog.new(@frame, :message => "Save Geometry", :caption => "Specify name of geometry:")
+       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)
+         rescue Exception => e
+           error_dialog(e)
+         end
+       end 
+     else
+       error_dialog("No geometry selected.")
+     end
+   end
+
+   # Display an error dialog for the exception
+   def error_dialog(exception)
+     message = if exception.is_a? String
+       exception
+     elsif exception.is_a? Exception
+       exception.message + "\n\n" + exception.backtrace[0..2].join("\n")
+     end
+     puts message
+     MessageDialog.new(@frame, message, "Error", Wx::ICON_ERROR).show_modal
+   end
+   
+   def save_image
+
+     begin
+       page = @notebook.get_current_page
+       if (page.respond_to? :image) 
+         image = page.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
+   	end
+
+end
+end
+