aims_project_windows 0.3.1

data/skeleton/config/tasks.rb

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+require 'stringio'
+
+# ====================================================
+# These are capistrano tasks to help with queueing calculations
+# on a remote computing-cluster, tracking their status
+# and retreiving calculation outputs.
+# ====================================================
+
+def _cset(name, *args, &block)
+  unless exists?(name)
+    set(name, *args, &block)
+  end
+end
+
+# logs the command then executes it locally.
+# returns the command output as a string
+def run_locally(cmd)
+  logger.trace "executing locally: #{cmd.inspect}" if logger
+  output_on_stdout = nil
+  elapsed = Benchmark.realtime do
+    output_on_stdout = `#{cmd}`
+  end
+  if $?.to_i > 0 # $? is command exit code (posix style)
+    raise Capistrano::LocalArgumentError, "Command #{cmd} returned status code #{$?}"
+  end
+  logger.trace "command finished in #{(elapsed * 1000).round}ms" if logger
+  output_on_stdout
+end
+  
+# =========================================================================
+# These variables must be set in the client Capfile. Failure to set them 
+# will result in an error.
+# =========================================================================
+_cset(:project_name) {abort "Please specify the project name, set :project_name, 'foo'"}
+_cset(:remote_project_dir) {abort "Please specify the name of the remote directory for this project, set :remote_project_dir, 'foo'"}
+# _cset(:staging_dir) {}
+# _cset(:qsub) {abort "Please specify the queue submission script to use for each calculation, set :qsub, 'foo'"}
+
+# =========================================================================
+# These variables may be set in the client capfile if their default values
+# are not sufficient.
+# =========================================================================
+_cset :aims_script, "aims.sh"
+
+# =========================================================================
+# These variables should NOT be changed unless you are very confident in
+# what you are doing. Make sure you understand all the implications of your
+# changes if you do decide to muck with these!
+# =========================================================================
+
+  namespace :aims do 
+
+    desc <<-DESC
+    Up-sync project with data transfer server
+    DESC
+    task :upsync, :roles => :data_transfer do 
+      # Verify this AimsProject can be loaded
+      project = AimsProject::Project.load(project_name)
+      find_servers(:roles => :data_transfer).each do |s|
+        # Upsync to remote directory
+        puts "Upsyncing project to #{s}..."
+        run_locally "rsync -auvz #{project.full_path} #{s}:#{remote_project_dir}/"
+      end
+    end
+    
+    desc <<-DESC
+    Down-sync project with data transfer server
+    DESC
+    task :downsync, :roles => :data_transfer do
+      # Verify this AimsProject can be loaded
+      project = AimsProject::Project.load(project_name)
+
+      find_servers(:roles => :data_transfer).each do |s|
+        # Downsync from remote directory
+        puts "Retreiving new data from #{s}"
+        run_locally "rsync -auvz #{s}:#{remote_project_dir}/#{project.relative_path}/ #{project.full_path}/"
+      end      
+    end
+
+    desc <<-DESC
+    Synchronize with the remote computation cluster.
+    DESC
+    task :synchronize, :roles => :data_transfer do 
+      # Verify this AimsProject can be loaded
+      project = AimsProject::Project.load(project_name)
+      upsync
+      downsync
+    end
+
+    task :env, :roles => :queue_submission do 
+      run "env"
+    end
+    
+    task :qstat, :roles => :queue_submission do
+      find_servers(:roles => :queue_submission).each do |s|
+        # Upsync to remote directory
+        stream qstat_cmd
+      end
+      
+    end
+
+    # Trigger a synchronize before enqueue
+    before "aims:enqueue", "aims:synchronize"
+
+    desc <<-DESC
+    Enqueue all staged calculations.  
+    This task will:
+    1) Customize and upload the script aims.sh to the remote server
+    2) cd to the calculation directory on the remote host
+    3) execute the "qsub" command as defined in Capfile
+    
+    Example usage: 
+    cap aims:enqueue 
+    DESC
+    task :enqueue, :roles => :queue_submission do 
+      
+      #  Load the project
+      project = AimsProject::Project.load(project_name)
+
+      # Enqueue all staged calculations
+      project.calculations.find_all{|calc| 
+        calc.status == AimsProject::STAGED
+        }.each do |calc|
+
+          # Define the remote calculation directory
+          remote_calc_dir = "#{remote_project_dir}/#{project.relative_path}/#{calc.relative_path}"
+
+          # Upload the aims.sh script to the calculation directory
+          upload File.join(AimsProject::CONFIG_DIR, aims_script), File.join(remote_calc_dir, aims_script) 
+
+
+          run <<-CMD
+          cd #{remote_calc_dir};
+          #{qsub}
+          CMD
+
+          # TODO, do this first, and then revert inside rollback
+          calc.status = AimsProject::QUEUED
+          calc.save
+
+        end
+      end
+
+      
+    end

data/skeleton/config/user_variables.rb

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+
+#
+# Put user defined variables here
+# These variables will be evaulated and used when
+# generating geometry.in and control.in for calculations.
+#
+# 
+#
+# An example usage is 
+#   
+#   @lattice_const = 5.9
+#   @k_grid = "2 2 2"
+#
+#
+# Then include these in any geometry file using embedded ruby
+#
+#   lattice_vector <%= [@lattice_const/2, @lattice_const/2, 0].join(" ") %>
+#   lattice_vector <%= [@lattice_const/2, 0, @lattice_const/2].join(" ") %>
+#   lattice_vector <%= [0, @lattice_const/2, @lattice_const/2].join(" ") %>
+#
+# And in any control.in file 
+#
+#   k_grid <%= @k_grid %>
+#
+# The <%=  %> start and end tags can contain any ruby code
+# Use <% %> start and end tags for ruby code whose output should be suppressed
+# Note the '@' at the front of all variables.  This is necessary in the user_variables file 
+#
+# Parameters can be specified on the command line of AimsCalc as follows:
+# 
+#   AimsCalc create some_geometry_file some_control_file lattice_const=5.7 k_grid="2 2 2"
+#
+# The root calculation directory will then have a sub directory with the calculation named
+#   lattice_const=5.7,k_grid=2_2_2
+# Notice that variables are concatenated with a comma and spaces are replaced with underscores. 
+# Only variables specified on the command line generate calculation sub-directories.  This 
+# is to enable 

data/skeleton/control/example.erb

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+# 
+# This is an example control file
+#
+
+# Keywords understood by aims can be specified like normal
+<% control_defaults %>
+xc                 pbe
+spin               none
+relativistic       atomic_zora scalar
+charge             0.
+
+# 
+# Mixing Parameters
+#
+occupation_type    gaussian 0.1
+mixer              pulay
+    preconditioner kerker 1.0
+    n_max_pulay        10
+    charge_mix_param   0.2  
+
+#
+# Convergence Accuracy
+#
+sc_accuracy_rho    1E-4
+sc_accuracy_eev    1E-2
+sc_accuracy_etot   1E-5
+sc_accuracy_forces 1E-3
+sc_iter_limit      100
+
+
+#
+#  Relaxation
+#
+#
+relax_geometry   bfgs 2.e-2
+restart_relaxations .true.
+<%= relax_geometry true %>
+
+# Include species like this
+<%= species 15, "light" %>
+<%= species 49, "light" %>

data/skeleton/geometry/example

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+atom 0 0 0 Si

metadata

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+--- !ruby/object:Gem::Specification
+name: aims_project_windows
+version: !ruby/object:Gem::Version
+  version: 0.3.1
+  prerelease: 
+platform: ruby
+authors:
+- Joshua Shapiro
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-05-30 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: wxruby-ruby19
+  requirement: &5625090 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *5625090
+- !ruby/object:Gem::Dependency
+  name: ruby-opengl
+  requirement: &5624860 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.60.3
+  type: :runtime
+  prerelease: false
+  version_requirements: *5624860
+- !ruby/object:Gem::Dependency
+  name: aims
+  requirement: &5624630 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *5624630
+- !ruby/object:Gem::Dependency
+  name: highline
+  requirement: &5624400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.11
+  type: :runtime
+  prerelease: false
+  version_requirements: *5624400
+- !ruby/object:Gem::Dependency
+  name: capistrano
+  requirement: &5624170 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.11.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *5624170
+description: This gem simplifies and streamlines the calculation pipeline for FHI-AIMS.
+email: joshua.shapiro@gmail.com
+executables:
+- AimsProjectManager
+- AimsCalc
+- AimsProject
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/aims_project/aims_project_exception.rb
+- lib/aims_project/aims_project_geometry.rb
+- lib/aims_project/app_controller.rb
+- lib/aims_project/atom.rb
+- lib/aims_project/calculation.rb
+- lib/aims_project/calculation_tree.rb
+- 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
+- lib/aims_project/inspector.rb
+- lib/aims_project/material.rb
+- lib/aims_project/octree.rb
+- lib/aims_project/project.rb
+- lib/aims_project/project_tree.rb
+- lib/aims_project/thread_callback_event.rb
+- lib/aims_project.rb
+- lib/aims_project/pan.gif
+- lib/aims_project/rotate.gif
+- lib/aims_project/zoom.gif
+- lib/aims_project/green_arrow.jpg
+- skeleton/Capfile
+- skeleton/config/aims.sh
+- skeleton/config/tasks.rb
+- skeleton/config/user_variables.rb
+- skeleton/control/example.erb
+- skeleton/geometry/example
+- README
+- bin/AimsProjectManager
+- bin/AimsCalc
+- bin/AimsProject
+homepage: https://github.com/jns/AimsProject
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ~>
+    - !ruby/object:Gem::Version
+      version: 1.9.2
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: This gem simplifies and streamlines the calculation pipeline for FHI-AIMS.
+test_files: []
+has_rdoc: