topas-tools 0.1.1 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ebd3b0096d76533b4ad2b3b29d13e9c0fb440ec2
-  data.tar.gz: 3f9822ab33d2135dda7593b0d7fcea801feef74f
+  metadata.gz: 5ad5733a79ab858d041879381d154d5d4035b1d5
+  data.tar.gz: 6ac694b38871a0953ff1c98c6eed806418800f50
 SHA512:
-  metadata.gz: 391701df3da48ef07f27893af04a5aa73deaad6bfc4782b5691d9e2991e861fb1da4b153ecdab7d5be71448f7f61a1eb8976ab29b7d94ba691277dc89b35fdd1
-  data.tar.gz: 2175813c9d94dcd5593b8796d4229607a63aedb09bc3e5adf280e0256651b80dedb7d820e6b9bf2bebc6d2d1a8db2209cb0b8ba69190700354f672931e5937fb
+  metadata.gz: edf7529c615d17dc0574b31f0e9777ad18e7c481e2f501207fd892c873c9c7dc1f656cb52ce3a446efb6e65cc1cb4c32f59b1e7b5fd08e5cc6ad7754c2d01bf1
+  data.tar.gz: 20999ca2835dd96b60939b29ded5430aca43cfa3e2999eda1db4884f314aaf62193f7f7ece0d0cc666bfab8f1830e3cdd4c0ec062de32f8d08cb1d03e6ba8080

data/bin/toparun

@@ -5,14 +5,14 @@ require 'optparse'
 require 'topas-tools'
 
 
-options = {points:[100.0, 16.0, 0.0], steps:[4.0, 1.0], smart:false,  system: :wine}
+options = {points:[100.0, 15.0, 0.25], steps:[4.0, 1.0], smart:false,  system: :wine, topasdir:'/home/dmitrienka/.wine/drive_c/TOPAS4-2/'}
 OptionParser.new do |opts|
-  opts.banner = "Usage: toparun.rb  [-p 100,15,0 -s 1,0.25] filename.inp"
+  opts.banner = "Usage: toparun.rb  [-p 100,15,0.25 -s 4,1] filename.inp"
   opts.on("-p", "--points LIST", Array ,"Array of points, representing intervals with different stepsizes"){|list|
     options[:points] = list.map(&:to_f)}
   opts.on("-s", "--steps LIST", Array ,"Well, stepsizes for that intervals"){|list|
     options[:steps] = list.map(&:to_f)}
-  opts.on("-s", "--[no-]smart", "Gone smart!") do |s|
+  opts.on("-S", "--[no-]smart", "Gone smart!") do |s|
     options[:smart] = s
   end
   opts.on("--system [SYS]", [:windows, :wine, :dummy],
@@ -23,12 +23,11 @@ end.parse!
 
 ARGV[0] || raise("Rrrr! Where is my input file??")
 
-TopasEngine.system = options[:system]
-
-
-runner = TopasEngine.new
-input = TopasInput.new IO.read(ARGV[0], :encoding => "UTF-8"), 
-                       ARGV[0].sub(/\..{2,3}$/, '')
-
-runner.refine input,  options[:points], options[:steps],  (options[:smart] ? QuantileAnalyzer.new : BaseAnalyzer.new)
-
+dir    = File.expand_path  File.dirname ARGV[0]
+name   = File.basename(ARGV[0], File.extname(ARGV[0]))
+text   = IO.read(ARGV[0],  :encoding => "UTF-8")
+engine = TopasEngine.create  options[:system], options[:topasdir]
+input  = TopasInput.new text, name
+steps  = Steps.new options[:points], options[:steps]
+runner = Metarefine.new engine, input, dir, steps 
+runner.toparun BaseAnalyzer.new

data/bin/toparunGUI

@@ -8,7 +8,7 @@ require 'topas-tools'
 Shoes.app :width => 400, :height => 800  do
 
   @log = StringIO.new
-  @log.write "Hi, log starts here!\n"
+  @log.write "k1\tR_wp\tMax dev.\tMultiplier\tOutlier\n"
     
   #base flow
   flow  :margin=>10 do
@@ -39,7 +39,7 @@ Shoes.app :width => 400, :height => 800  do
       end
 
       flow do
-        para "Stepss:"
+        para "Steps:"
         @stepsline = edit_line
         @stepsline.text = "4,1"
       end
@@ -59,11 +59,17 @@ Shoes.app :width => 400, :height => 800  do
         end
         
         Thread.new(points, steps, @log ) do  |points, steps|
-          inp = @inpline.text
+
+          inp    = @inpline.text
+          dir    = File.expand_path  File.dirname inp
+          name   = File.basename(inp, File.extname(inp))
+          text   = IO.read(inp,  :encoding => "UTF-8")
           engine = TopasEngine.create  @systemlist.text.to_sym, @topasdir.text
-          input = TopasInput.new IO.read(inp, :encoding => "UTF-8"),  inp
-          runner = Metarefine.new engine, input, File.dirname(inp), Steps.new(points, steps)
-          runner.toparun  BaseAnalyzer.new(@log)
+          input  = TopasInput.new text, name
+          steps  = Steps.new points, steps
+          runner = Metarefine.new engine, input, dir, steps 
+          runner.toparun BaseAnalyzer.new(@log)
+
           @clear = button 'Clear' do
             @log = StringIO.new
             @clear.clear
@@ -71,9 +77,8 @@ Shoes.app :width => 400, :height => 800  do
         end
       end
   
-        para self
       caption "Log:"
-      stack :width => 300,   :margin => 20 do
+      stack :width => 370,   :margin => 20 do
  
  
          @paralog = para

data/lib/topas-tools/Analyzers.rb

@@ -1,17 +1,55 @@
 class BaseAnalyzer
+
+K1TABLE = [5.62619251369954 ,3.59689767105988, 2.99683950381941, 2.9141936236358 , 3.37232041437195 ,2.93196313616901, 2.72771585462825, 2.70417682172506, 2.86576896853064 ,2.66921102377684, 2.57092705221669, 2.55881443841962, 2.64995441497466 ,2.53075618782533, 2.47791909362932, 2.4741828679544 , 2.53384546494551 ,2.45983379319381, 2.4212286638301 , 2.4159429171073 , 2.45784825894735 ,2.40879237590095, 2.38090443345185, 2.38216835038994, 2.41048201093783 ,2.36989342570794, 2.35215022384351, 2.3524695182014, 2.37772035649117 ,2.34643406722578, 2.33269558844597, 2.33379314746303, 2.35213581186961 ,2.3293126888992 , 2.31585973838799, 2.32211834728897, 2.33719246258054 ,2.31822219208683, 2.30836925652429, 2.30928647548234, 2.32053355883361 ,2.30880999917026, 2.29983955811199, 2.30081635190135, 2.31427557030017 ,2.29827012906655]
+
   def initialize output = $stdout
     @out = output
     @count = 0
+    @rtable = []
   end
   
   def analyze inp
-    @out.print "Analizing #{inp.name}... \n"
+    restrains = inp.restrains
+    restrains.each do |r|
+      @rtable << {k1:inp.k1, r_wp:inp.r_wp, name:r[:name],
+                  delta:(r[:value] - r[:restrain])}
+    end
+    @name = inp.base_name
+    errors = restrains.map{|r| r[:value] - r[:restrain]}
+    mdev = max_dev(errors)
+    mult = K1TABLE[restrains.size - 5]
+    outlier = (mdev > mult ? "x" : "o")
+    @out.print "%d\t%0.3f\t%0.3f\t%0.3f\t#{outlier}\n" % [inp.k1, inp.r_wp, mdev, mult]
     @count = @count + 1
     true
   end
+
   
   def report 
     @out.print "Refinement  was finished in #{@count} steps.\n"
+    file = File.open("#{@name}_rtable.dat", 'w')
+    file.write("K1\tRwp\tBond\tDelta\tError\n")
+    @rtable.each do |rt|
+      file.write("#{rt[:k1]}\t#{rt[:r_wp]}\t#{rt[:name]}\t#{rt[:delta]}\t0\n")
+    end
+    file.close
     true
   end
+  
+  private
+  
+  def quantile7 p, x
+    n = x.size
+    sorted = x.sort
+    j = (n*p - p +1).floor
+    g = n*p - p + 1 - j
+    (1 - g) * sorted[j - 1] + g * sorted[j]
+  end
+
+  def max_dev x
+    q1 = quantile7 0.25, x
+    q3 = quantile7 0.75, x
+    iqr = q3 - q1
+    [(q1 - x.min)/iqr, (x.max-q3)/iqr].max
+  end
 end

data/lib/topas-tools/Metarefine.rb

@@ -27,10 +27,10 @@ class Metarefine
   def toparun analyzer, work_dir = File.expand_path(@input.base_name)
     Dir.mkdir(work_dir) unless Dir.exists? work_dir
     @steps.k1s.reduce(@input) do |inp, k1|
-      out = @engine.tc work_dir inp.set_k1(k1)
+      out = @engine.tc work_dir, inp.set_k1(k1)
       analyzer.analyze(out) ? out : break
     end
-    Dir.chdir @base_dir
+    Dir.chdir @basedir
     analyzer.report
   end
 end

data/lib/topas-tools/TopasInput.rb

@@ -5,9 +5,10 @@ class TopasInput
     @base_name  = get_base_name base_name
     @name = get_name
     @restrains = get_restrains
+    @r_wp = get_rwp
   end
 
-  attr_reader :k1, :name, :base_name, :restrains, :text
+  attr_reader :k1, :name, :base_name, :restrains, :text, :r_wp
  
  
   def set_k1!(num)
@@ -48,6 +49,11 @@ class TopasInput
     @text.scan(/penalties_weighting_K1\s+([\d.]+)/)[0][0].to_f
   end
 
+  def get_rwp
+    @text.scan(/r_wp\s+([\d.]+)/)[0][0].to_f
+  end
+
+
   def get_base_name bn
     if   bn
       base_name = File.basename(bn, File.extname(bn))

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: topas-tools
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - Artem Dmitrienko