eulim 0.0.13 → 0.0.14

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -43,8 +43,9 @@ Or install it yourself as:
 
 ### Reaction
 
-* attributes: equation, is_valid, is_balanced, species
-* methods: new("Put your reaction string here") #For eg: ('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)')
+* attributes: equation, is_valid, is_balanced, species, balanced_eqn
+* methods: new(equation: "Put your reaction string here", rate_equation: "r_{CaCo3} = k[CaO]")
+* For eg: (equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)', rate_equation: "rNa = k[HCl]")
 
 ## Usage
 ```bash
@@ -60,19 +61,22 @@ $ Eulim::Chemistry::Element.get_by_name "helium" # or "Helium"
 $ Eulim::Chemistry::Compound.new("CaCO3")
 => #<Eulim::Chemistry::Compound:0x00000002a65340 @formula="CaCO3", @constituents={"Ca"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c805a8 @name="Calcium", @symbol="Ca", @atomic_number=20, @atomic_mass=#<Unitwise::Measurement value=40.078 unit=u>>, :atom_count=>1}, "C"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c8f6e8 @name="Carbon", @symbol="C", @atomic_number=6, @atomic_mass=#<Unitwise::Measurement value=12.0107 unit=u>>, :atom_count=>1}, "O"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c8dc30 @name="Oxygen", @symbol="O", @atomic_number=8, @atomic_mass=#<Unitwise::Measurement value=15.9996 unit=u>>, :atom_count=>3}}, @molecular_mass=#<Unitwise::Measurement value=100.0875 unit=u>>
 
-$ Eulim::Chemistry::Reaction.new('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').equation
+$Eulim::Chemistry::Reaction.new(equation: 'KMnO4 + HCl >> KCl + MnCl2 + H2O + Cl2').balanced_eqn
+ => "2KMnO4 + 16HCl >> 2KCl + 2MnCl2 + 8H2O + 5Cl2"
+
+$ Eulim::Chemistry::Reaction.new(equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').equation
  => "2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)" 
  
-$ Eulim::Chemistry::Reaction.new('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').is_valid
+$ Eulim::Chemistry::Reaction.new(equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').is_valid
 => true 
  
-$ Eulim::Chemistry::Reaction.new('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').is_balanced
+$ Eulim::Chemistry::Reaction.new(equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').is_balanced
 => true 
  
-$ Eulim::Chemistry::Reaction.new('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').species
+$ Eulim::Chemistry::Reaction.new(equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)').species
 => {:reactants=>{"Na"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002ca6910 @formula="Na", @constituents={"Na"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c88e10 @name="Sodium", @symbol="Na", @atomic_number=11, @atomic_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :stoichiometry=>2, :state=>"solid"}, "HCl"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002c90ed0 @formula="HCl", @constituents={"H"=>{:element=>#<Eulim::Chemistry::Element:0x000000025e5ab8 @name="Hydrogen", @symbol="H", @atomic_number=1, @atomic_mass=#<Unitwise::Measurement value=1.0079 unit=u>>, :atom_count=>1}, "Cl"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c82c90 @name="Chlorine", @symbol="Cl", @atomic_number=17, @atomic_mass=#<Unitwise::Measurement value=35.453 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=36.4609 unit=u>>, :stoichiometry=>2, :state=>"aqueous"}}, :products=>{"NaCl"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002c73bf0 @formula="NaCl", @constituents={"Na"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c88e10 @name="Sodium", @symbol="Na", @atomic_number=11, @atomic_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :atom_count=>1}, "Cl"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c82c90 @name="Chlorine", @symbol="Cl", @atomic_number=17, @atomic_mass=#<Unitwise::Measurement value=35.453 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=58.4427 unit=u>>, :stoichiometry=>2, :state=>"aqueous"}, "H2"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002c34180 @formula="H2", @constituents={"H"=>{:element=>#<Eulim::Chemistry::Element:0x000000025e5ab8 @name="Hydrogen", @symbol="H", @atomic_number=1, @atomic_mass=#<Unitwise::Measurement value=1.0079 unit=u>>, :atom_count=>2}}, @molecular_mass=#<Unitwise::Measurement value=2.0158 unit=u>>, :stoichiometry=>1, :state=>"gaseous"}}}
 
-$ Eulim::Chemistry::Reaction.new('2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)')
+$ Eulim::Chemistry::Reaction.new(equation: '2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)')
 => #<Eulim::Chemistry::Reaction:0x00000002ce22f8 @equation="2Na(s) + 2HCl(aq) >> 2NaCl(aq) + H2(g)", @species={:reactants=>{"Na"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002ce1d80 @formula="Na", @constituents={"Na"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c88e10 @name="Sodium", @symbol="Na", @atomic_number=11, @atomic_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :stoichiometry=>2, :state=>"solid"}, "HCl"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002cabdc0 @formula="HCl", @constituents={"H"=>{:element=>#<Eulim::Chemistry::Element:0x000000025e5ab8 @name="Hydrogen", @symbol="H", @atomic_number=1, @atomic_mass=#<Unitwise::Measurement value=1.0079 unit=u>>, :atom_count=>1}, "Cl"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c82c90 @name="Chlorine", @symbol="Cl", @atomic_number=17, @atomic_mass=#<Unitwise::Measurement value=35.453 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=36.4609 unit=u>>, :stoichiometry=>2, :state=>"aqueous"}}, :products=>{"NaCl"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002c8cda8 @formula="NaCl", @constituents={"Na"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c88e10 @name="Sodium", @symbol="Na", @atomic_number=11, @atomic_mass=#<Unitwise::Measurement value=22.9897 unit=u>>, :atom_count=>1}, "Cl"=>{:element=>#<Eulim::Chemistry::Element:0x00000002c82c90 @name="Chlorine", @symbol="Cl", @atomic_number=17, @atomic_mass=#<Unitwise::Measurement value=35.453 unit=u>>, :atom_count=>1}}, @molecular_mass=#<Unitwise::Measurement value=58.4427 unit=u>>, :stoichiometry=>2, :state=>"aqueous"},"H2"=>{:compound=>#<Eulim::Chemistry::Compound:0x00000002c6f938 @formula="H2", @constituents={"H"=>{:element=>#<Eulim::Chemistry::Element:0x000000025e5ab8 @name="Hydrogen", @symbol="H", @atomic_number=1, @atomic_mass=#<Unitwise::Measurement value=1.0079 unit=u>>, :atom_count=>2}}, @molecular_mass=#<Unitwise::Measurement value=2.0158 unit=u>>, :stoichiometry=>1, :state=>"gaseous"}}}, @is_valid=true, @is_balanced=true> 
 ```
 ## Development

data/eulim.gemspec

@@ -38,7 +38,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'rake', '~> 10.0'
   spec.add_development_dependency 'rspec', '~> 3.0'
   spec.add_development_dependency 'rubocop', '~>0.49.1'
-
-  spec.add_dependency 'require_all', '~> 1.4.0'
-  spec.add_dependency 'unitwise', '~> 2.1.0'
+  spec.add_dependency             'unitwise', '~>2.1.0'
+  spec.add_dependency             'rubypython', '~> 0.6.4'
+  spec.add_dependency             'require_all', '~> 1.4.0'
 end

data/lib/eulim.rb

@@ -11,10 +11,11 @@ Ch    =   Eulim::Chemistry
 Elem  =   Ch::Element
 Comp  =   Ch::Compound
 Rxn   =   Ch::Reaction
-Subs  =   Ch::Substance
+Sub   =   Ch::Substance
 
 Cl    =   Eulim::Chemical
 Rcts  =   Cl::Reactors
+Rct   =   Rcts::Reactor
 Br    =   Rcts::Batch
 Cstr  =   Rcts::CSTR
 Pfr   =   Rcts::PFR

data/lib/eulim/chemical/reactors/continuous_stirred_tank_reactor.rb

@@ -7,6 +7,18 @@ module Eulim
           super args
         end
 
+        def find_volume
+          # accumulation is zero
+          compound_formula = @reaction.rate_equation.split(' ').first.split('r').last
+          ci = @input[:substance].species[compound_formula]
+          co = @output[:substance].species[compound_formula]
+          input = @input[:quantity] * ci[:weight_percent] /
+                  (100 * ci[:compound].molar_mass)
+          output = @output[:quantity] * co[:weight_percent] /
+                   (100 * co[:compound].molar_mass)
+          x = (input - output) / input
+        end
+
         def self.humanized_name
           'Continuous stirred-tank reactor'
         end

data/lib/eulim/chemical/reactors/reactor.rb

@@ -3,12 +3,36 @@ module Eulim
     module Reactors
       # This is the base class for the diff kinds of reactors
       class Reactor
-        attr_accessor :system, :volume, :input, :output, :conversion
+        attr_reader :system, :volume, :input, :output, :reaction
+
+        # ATTRS = [:system, :volume, :input, :output, :rate_equation]
 
         def initialize(args = {})
-          @volume = volume_if_valid(args[:volume]) if args[:volume]
-          @system = args[:system] || :open
-          @input = input_if_valid(args[:input]) if args[:input]
+          self.system = args[:system]
+          self.volume = args[:volume] if args[:volume]
+          self.input = args[:input] if args[:input]
+          self.output = args[:output] if args[:output]
+          self.reaction = args[:reaction] if args[:reaction]
+        end
+
+        def system=(sys)
+          @system = sys || :open
+        end
+
+        def volume=(vol)
+          @volume = volume_if_valid vol
+        end
+
+        def input=(inp)
+          @input = feed_if_valid inp
+        end
+
+        def output=(out)
+          @output = feed_if_valid out
+        end
+
+        def reaction=(rxn)
+          @reaction = reaction_if_valid rxn
         end
 
         private
@@ -23,20 +47,30 @@ module Eulim
           raise ArgumentError, 'Invalid volume unit'
         end
 
-        def input_if_valid(inp)
-          raise ArgumentError, 'Invalid input substance' if inp[:substance].class != Subs
+        def feed_if_valid(f)
+          raise ArgumentError, 'Invalid substance' if f[:substance].class != Sub
           begin
-            inp[:quantity] = Unitwise inp[:quantity]
+            f[:quantity] = Unitwise f[:quantity]
           rescue
-            raise ArgumentError, 'Invalid input quantity'
+            raise ArgumentError, 'Invalid quantity'
           end
-          dim = inp[:quantity].composition.to_h
-          return inp if valid_input_quantity_compositions.include? dim
-          raise ArgumentError, 'Invalid input quantity unit'
+          dim = f[:quantity].composition.to_h
+          return f if valid_feed_quantity_dimensions.include? dim
+          raise ArgumentError, 'Invalid quantity unit'
+        end
+
+        def valid_feed_quantity_dimensions
+          [{ 'M' => 1 }, { 'M' => 1, 'T' => -1 }]
         end
 
-        def valid_input_quantity_compositions
-          [{ 'M' => 1 }, { 'M' => 1, 'T' => -1 }, {}, { 'T' => -1 }]
+        def reaction_if_valid(r)
+          # raise ArgumentError, 'Substance not in reaction' if
+          #   @input && (
+          #     r.species[:reactants].keys &
+          #     @input[:substance].species.keys
+          #   ).empty?
+          return r if r.class == Rxn && r.is_valid
+          raise ArgumentError, 'Invalid reaction argument'
         end
       end
     end

data/lib/eulim/chemistry/compound.rb

@@ -8,22 +8,22 @@ module Eulim
       COMPOUND_REGEXP =
         /[A-Z][a-z]{0,2}\d*|\((?:[^()]*(?:\(.*\))?[^()]*)+\)\d*/
 
-      attr_accessor :molecular_mass, :constituents, :formula
+      attr_accessor :molecular_mass, :constituents, :formula, :molar_mass
 
       def initialize(arg)
         @formula = arg
         build_constituents
-        calculate_molecular_mass
+        calculate_mass
       end
 
       private
 
-      def calculate_molecular_mass
-        @molecular_mass = Unitwise(0, 'u')
+      def calculate_mass
+        @molecular_mass = Unitwise(0.0, 'u')
         @constituents.each do |_symbol, info|
           @molecular_mass += info[:element].atomic_mass * info[:atom_count]
         end
-        @molecular_mass
+        @molar_mass = Unitwise(@molecular_mass.value / 1000.0, 'kg/mol')
       end
 
       def build_constituents

data/lib/eulim/chemistry/reaction.rb

@@ -1,25 +1,42 @@
+require 'matrix'
+
 module Eulim
   module Chemistry
     # This class has functionality for reaction
     # Ex: check for balanced rxn, validity of a rxn
     class Reaction
-      attr_accessor :equation, :is_valid, :is_balanced, :species
+      attr_accessor :equation, :is_valid, :species, :participants, :balanced_eqn, :rate_equation
 
       STATES = {
         '(s)' => 'solid', '(l)' => 'liquid',
         '(g)' => 'gaseous', '(aq)' => 'aqueous',
-        '' => 'liquid'
+        '' => ''
       }.freeze
 
-      def initialize(arg)
-        @equation = arg
+      def initialize(args)
+        # rate_eqn should be of the form: 'r_{CaO} = k[CaO][CO2]'
+        @equation = args[:equation]
         @species = build_species
         @is_valid = valid_rxn?
-        @is_balanced = balanced_rxn?
+        p participant_elements
+        # @balanced_eqn = balance_rxn
+        @rate_equation = validify_rate_eqn args[:rate_equation]
       end
 
       private
 
+      def validify_rate_eqn(rate_eqn)
+        if rate_eqn
+          rate_eqn.gsub('_{', '')
+                  .gsub('}', '')
+                  .gsub('[', ' * c')
+                  .gsub(']', '')
+        else
+          specie = @species[:reactants].keys.first
+          'r' + specie + ' = k * c' + specie
+        end
+      end
+
       def build_species
         r = {}
         result = {}
@@ -81,6 +98,61 @@ module Eulim
       def get_state(specie)
         specie.match(/\((s|l|g|aq)\)$/).to_s
       end
+
+      def participant_elements
+        participants = []
+        @species[:reactants].keys.each do |r|
+          participants << @species[:reactants][r][:compound].constituents.keys
+        end
+        @participants = participants.flatten.uniq
+      end
+
+      def get_participant_row(parti)
+        row = []
+        @species.keys.each do |key|
+          i = key == :reactants ? 1 : -1
+          @species[key].keys.each do |specie|
+            if specie.include? parti
+              row << @species[key][specie][:compound]
+                     .constituents[parti][:atom_count] * i
+            else
+              row << 0
+            end
+          end
+        end
+        row
+      end
+
+      def write_matrix
+        @matrix = Matrix[]
+        @participants.each do |parti|
+          @matrix = Matrix.rows(@matrix.to_a << get_participant_row(parti))
+        end
+        @matrix
+      end
+
+      def balanced_coeff_array
+        write_matrix
+        null_space_array = @matrix.nullspace_array
+        lcm = null_space_array.collect(&:denominator).reduce(1, :lcm)
+        null_space_array.collect { |x| (x * lcm).to_i }
+      end
+
+      def balance_rxn
+        exp = ''
+        i = 0
+        bal_coeff = balanced_coeff_array
+        @species.keys.each do |key|
+          @species[key].keys.each do |comp|
+            coeff = bal_coeff[i] == 1 ? ' ' : ' ' + bal_coeff[i].abs.to_s
+            state = STATES.key(@species[key][comp][:state])
+            exp = exp + coeff + comp + state + ' +'
+            i += 1
+          end
+          exp = key == :reactants ? exp.chomp('+') + '>>' : exp.chomp('+')
+        end
+        exp.strip
+      end
     end
   end
 end

data/lib/eulim/version.rb

@@ -1,3 +1,3 @@
 module Eulim
-  VERSION = '0.0.13'.freeze
+  VERSION = '0.0.14'.freeze
 end

data/lib/matrix.rb

@@ -0,0 +1,20 @@
+require 'rubypython'
+# this class is extension of Matrix class offered by ruby
+class Matrix
+  def nullspace_as_string
+    a = to_a
+    RubyPython.start
+    main = RubyPython.import('__main__')
+    RubyPython::Python.PyRun_SimpleString <<-PYTHON
+from sympy import Matrix
+import numpy as np
+def null_space(a):
+  return np.array_str(np.array(Matrix(a).nullspace()))
+    PYTHON
+    main.null_space(a).rubify
+  end
+
+  def nullspace_array
+    nullspace_as_string[2..-3].split(' ').map(&:to_r)
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: eulim
 version: !ruby/object:Gem::Version
-  version: 0.0.13
+  version: 0.0.14
 platform: ruby
 authors:
 - Syed Fazil Basheer
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-06-30 00:00:00.000000000 Z
+date: 2017-07-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -68,33 +68,47 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.49.1
 - !ruby/object:Gem::Dependency
-  name: require_all
+  name: unitwise
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.4.0
+        version: 2.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.4.0
+        version: 2.1.0
 - !ruby/object:Gem::Dependency
-  name: unitwise
+  name: rubypython
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: 0.6.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.1.0
+        version: 0.6.4
+- !ruby/object:Gem::Dependency
+  name: require_all
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.4.0
 description: A gem for scientific data.
 email:
 - fazil.basheer@quester.xyz
@@ -133,6 +147,7 @@ files:
 - lib/eulim/structures/pipe.rb
 - lib/eulim/structures/structure.rb
 - lib/eulim/version.rb
+- lib/matrix.rb
 - lib/string.rb
 homepage: https://github.com/syedfazilbasheer-quester/eulim-gem
 licenses: