crystalcell 0.1.0 → 0.1.1
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- checksums.yaml +4 -4
- data/CHANGES +6 -0
- data/VERSION +1 -1
- data/crystalcell.gemspec +3 -3
- data/lib/crystalcell/cell.rb +21 -3
- data/lib/crystalcell/povray.rb +8 -7
- data/lib/crystalcell/povray/cell.rb +93 -30
- data/lib/crystalcell/povray/sphere.rb +10 -3
- data/lib/crystalcell/povray/triangle.rb +5 -8
- data/test/povray/test_cell.rb +118 -27
- data/test/povray/test_tetrahedron.rb +8 -8
- data/test/povray/test_triangle.rb +2 -2
- data/test/test_cell.rb +91 -71
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: f9397d63b61597552c608dbef090bd1648bb5685
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data.tar.gz: 7b10b0f30d8552a5e6be3481e3735cad5d595ed2
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9392b319f43e8b50921e1fe25b4b4a4037d6c21d24f729290620b71be337f9b5631d2e1e3552ad7dbd42f1edc5ef0e1dfbb64f94b4233103c47cf0055b09e3ce
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data.tar.gz: b8deedf28f6e4a0420f3a7873119998ca0a6557ab9769a10e6e56e8b733ab8213d564883f050a4127ded7b133958a033c30e43f015106d4117b5df9c35e2a8a0
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data/CHANGES
CHANGED
@@ -2,6 +2,12 @@
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<!-- Master -->
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== Version 0.1.1 [2017-05-23] released
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* Add CrystalCell::Povray::Cell.bond
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* Add CrystalCell::atoms_of_element
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* Add name in CrystalCell::Cell.atoms_in_supercell
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== Version 0.1.0 [2016-07-12] released
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* Add Cell.to_povcell
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.1
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data/crystalcell.gemspec
CHANGED
@@ -2,16 +2,16 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: crystalcell 0.1.
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# stub: crystalcell 0.1.1 ruby lib
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Gem::Specification.new do |s|
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s.name = "crystalcell"
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s.version = "0.1.
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s.version = "0.1.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib"]
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s.authors = ["ippei94da"]
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s.date = "
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s.date = "2017-05-23"
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s.description = "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n And this provides simple treatment of a periodic boundary condition.\n "
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s.email = "ippei94da@gmail.com"
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s.extra_rdoc_files = [
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data/lib/crystalcell/cell.rb
CHANGED
@@ -99,13 +99,19 @@ class CrystalCell::Cell
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@atoms.collect{ |i| i.position }
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end
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-
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-
#index は原子の永続的な id ではない。
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# ブロックの評価が真になった原子の index を配列にして返す。
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#Array#select は index ではなく要素そのものを配列にして返すので、少し違う。
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#index は原子の永続的な id ではない。
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def select_indices( &block )
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return @atoms.select_indices( &block )
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end
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#元素情報が elem の原子を配列にまとめて返す。(not indices)
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def atoms_of_element(str)
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@atoms.select{ |i| i.element == str }
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end
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#Set element name to each atom in self.
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#Argument 'elems' is a list of new names, which has [] method. e.g.,
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# 1. Array, [ 'Li', 'O' ]
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@@ -139,10 +145,22 @@ class CrystalCell::Cell
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def atoms_in_supercell( a_min, a_max, b_min, b_max, c_min, c_max )
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results = []
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@atoms.each do |atom|
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#pp atom; exit
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a_min.upto( a_max ) do |a|
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b_min.upto( b_max ) do |b|
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c_min.upto( c_max ) do |c|
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-
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new_name = sprintf("%s-%d%d%d",
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atom.name,
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a + 5,
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b + 5,
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c + 5
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)
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results << CrystalCell::Atom.new(
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atom.element,
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(atom.position.to_v3di + [ a, b, c ].to_v3di).to_a,
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new_name
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)
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end
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end
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end
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data/lib/crystalcell/povray.rb
CHANGED
@@ -10,13 +10,14 @@ require 'crystalcell/povray/tetrahedron.rb'
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require 'crystalcell/povray/color.rb'
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DEFAULT_ENVIRONMENTS = [
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'background {color rgb<1,1,1>}',
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'light_source{ < 4, 1, 4 > color <1,1,1> parallel point_at 0 }',
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'default{ texture{ finish{ ambient 0.4 phong 1.0 phong_size 10 } } }',
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]
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class CrystalCell::Povray
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DEFAULT_ENVIRONMENTS = [
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'background {color rgb<1,1,1>}',
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'light_source{ < 4, 1, 4 > color <1,1,1> parallel point_at 0 }',
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'default{ texture{ finish{ ambient 0.4 phong 1.0 phong_size 10 } } }',
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]
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attr_reader :camera, :environments, :cell, :axes
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# camera_info indicates hash with the keys of camera info,
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@@ -60,7 +61,7 @@ class CrystalCell::Povray
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File.open(povfile, 'w') do |io|
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dump(io)
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end
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-
system "povray -D #{povfile}"
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+
system "povray -D #{povfile} > /dev/null"
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end
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# shoot 4 angles and unite.
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@@ -6,7 +6,11 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
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LATTICE_RADIUS = 0.02
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LATTICE_COLOR = [0.50, 0.50, 0.50]
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BOND_RADIUS = 0.05
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BOND_COLOR = [0.75, 0.75, 0.75]
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#BOND_COLOR = [0.75, 0.75, 0.75]
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class SizeError < StandardError; end
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class AtomNotFoundError < StandardError; end
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# povray 形式の文字列を返す。
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def to_pov
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@@ -22,43 +26,89 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
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# 原子を描画するための pov 形式文字列を返す。
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# 周期境界近傍の原子が tolerance 未満ならば、反対側のセル境界にも描画する。
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-
def atoms_to_povs(tolerance
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29
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+
def atoms_to_povs(tolerance: 0.0, transmit: nil)
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results = []
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atoms.each do |atom|
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periodic_translations(atom.position, tolerance).each do |translation|
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-
results << atom_to_pov(atom.translate(translation))
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results << atom_to_pov(atom: atom.translate(translation), transmit: transmit)
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#results << atom_to_pov(atom.translate(translation))
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35
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end
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end
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results
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end
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-
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-
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# Return povray format string to draw bond between two atoms.
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# contents should be like ['Na1', 'Cl2'] # (element + number)
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def bond(atomids)
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#pp atomids
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if atomids.size != 2
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raise SizeError
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end
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atoms = []
|
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atomids.each do |atomid|
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atom = atom_by_id(atomid)
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raise AtomNotFoundError, atomid unless atom
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atoms << atom
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end
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intermediate =
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(( atoms[0].position + atoms[1].position )/ 2.0) .to_v3d(self.axes)
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results = []
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atoms.each do |atom|
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cyl = CrystalCell::Povray::Cylinder.new(
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atom.position.to_v3d(self.axes),
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intermediate,
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BOND_RADIUS,
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CrystalCell::Povray::Element.color( atom.element)
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)
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results << cyl.to_pov
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end
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results.join("\n")
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end
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# Return povray format string to draw triangle among three atoms.
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# contents should be like ['Na1', 'Cl2', 'Cl3'] # (element + number from 1)
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# Color is set as 0th item in atomids
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def triangle(atomids)
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if atomids.size != 3
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raise SizeError
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+
end
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atoms = []
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atomids.each do |atomid|
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atom = atom_by_id(atomid)
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raise AtomNotFoundError, atomid unless atom
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atoms << atom
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end
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#pp atoms
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tri = CrystalCell::Povray::Triangle.new(
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*atoms.map { |atom| atom.position.to_v3d(self.axes)},
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CrystalCell::Povray::Element.color( atoms[0].element)
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)
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tri.to_pov
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end
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# Return povray format string to draw tetrahedron among four atoms.
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# contents should be like ['Na1', 'Cl2', 'Cl3', 'Cl4'] # (element + number from 1)
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# Color is set as 0th item in atomids
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def tetrahedron(atomids)
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if atomids.size != 4
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raise SizeError
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end
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atoms = []
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atomids.each do |atomid|
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atom = atom_by_id(atomid)
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raise AtomNotFoundError, atomid unless atom
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atoms << atom
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end
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#pp atoms
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tetra = CrystalCell::Povray::Tetrahedron.new(
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*atoms.map { |atom| atom.position.to_v3d(self.axes)},
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CrystalCell::Povray::Element.color( atoms[0].element)
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)
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tetra.to_pov
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end
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# 格子の棒を描画するための pov 形式文字列を返す。
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-
def lattice_to_povs
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+
def lattice_to_povs # should be changed to 'lattice'
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v000 = Vector3DInternal[ 0.0, 0.0, 0.0 ].to_v3d(self.axes)
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v001 = Vector3DInternal[ 0.0, 0.0, 1.0 ].to_v3d(self.axes)
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v010 = Vector3DInternal[ 0.0, 1.0, 0.0 ].to_v3d(self.axes)
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@@ -87,12 +137,25 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
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137
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results
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end
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139
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# Return atom from 'atom_id' like 'Na1' or 'Na1-556'.
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def atom_by_id(atom_id)
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elem_num, perio = atom_id.split('-')
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/^(\D+)(\d+)/ =~ elem_num
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elem = $1
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num = $2
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perio ||= '555'
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atom = atoms_of_element(elem)[num.to_i - 1]
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vec = perio.split(//).map { |figure| figure.to_i - 5 }
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atom.translate(vec.to_v3di)
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end
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private
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153
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92
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-
def atom_to_pov(atom)
|
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+
def atom_to_pov(atom:, transmit: nil)
|
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#def atom_to_pov(atom)
|
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color = CrystalCell::Povray::Element.color( atom.element)
|
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radius = CrystalCell::Povray::Element.draw_radius(atom.element) * RADIUS_RATIO
|
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-
Mageo::Sphere.new(atom.position.to_v3d(axes), radius).to_pov(color) +
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Mageo::Sphere.new(atom.position.to_v3d(axes), radius).to_pov(color: color, transmit: transmit) +
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" // #{atom.element}" + "\n"
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end
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@@ -3,9 +3,16 @@
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class Mageo::Sphere
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# povray 形式の文字列を返す。
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# color は Float による配列。通常、0〜1の範囲。
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-
def to_pov(color)
|
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-
sprintf(
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8
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-
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def to_pov(color: , transmit: nil)
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result = sprintf("object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} ", *position, radius)
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#sprintf( "object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} pigment {color rgb <%4.2f, %4.2f, %4.2f>} }",
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# *position, radius, *color)
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if transmit
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result += sprintf("pigment {color rgbt <%4.2f, %4.2f, %4.2f, %4.2f>} }", *color, transmit)
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else
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result += sprintf("pigment {color rgb <%4.2f, %4.2f, %4.2f>} }", *color)
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end
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end
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def dump(io)
|
@@ -13,16 +13,13 @@ class CrystalCell::Povray::Triangle < Mageo::Triangle
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# povray 形式の文字列を返す。
|
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14
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# color は Float による配列。通常、0〜1の範囲。
|
15
15
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def to_pov
|
16
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-
v = self.vertices
|
17
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-
|
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+
#v = self.vertices
|
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#sprintf( "object { cylinder{ <% 7.4f, % 7.4f, % 7.4f>, <% 7.4f, % 7.4f, % 7.4f>, %7.4f } pigment { color rgb <%4.2f, %4.2f, %4.2f> } }",
|
18
|
+
result = sprintf("triangle{ < % 7.4f, % 7.4f, % 7.4f>,<% 7.4f,% 7.4f,% 7.4f>,<% 7.4f,% 7.4f,% 7.4f>",
|
18
19
|
*@vertices[0], *@vertices[1], *@vertices[2])
|
19
|
-
result += sprintf(" pigment {color rgb<%
|
20
|
-
result += sprintf(" transmit %
|
20
|
+
result += sprintf(" pigment {color rgb<% 7.4f,% 7.4f,% 7.4f>", *@color)
|
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+
result += sprintf(" transmit % 7.4f", @transmit) if @transmit
|
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22
|
result += "}}"
|
22
|
-
#result = sprintf("triangle{<%f,%f,%f>,<%f,%f,%f>,<%f,%f,%f> " +
|
23
|
-
# "pigment {color rgb<%f,%f,%f>}}",
|
24
|
-
# *@vertices[0], *@vertices[1], *@vertices[2], *@color)
|
25
|
-
#
|
26
23
|
return result
|
27
24
|
end
|
28
25
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|
data/test/povray/test_cell.rb
CHANGED
@@ -2,6 +2,7 @@
|
|
2
2
|
# coding: utf-8
|
3
3
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|
4
4
|
require "helper"
|
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|
+
require "pp"
|
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6
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class TC_Povray_Sphere < Test::Unit::TestCase
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def setup
|
@@ -11,7 +12,11 @@ class TC_Povray_Sphere < Test::Unit::TestCase
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def test_to_pov
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assert_equal(
|
13
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"object { sphere{< 1.0000, 2.0000, 3.0000>, 2.0000} pigment {color rgb <0.30, 0.60, 0.90>} }",
|
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-
@s00.to_pov([0.3, 0.6, 0.9]) )
|
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@s00.to_pov(color: [0.3, 0.6, 0.9]) )
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+
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assert_equal(
|
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"object { sphere{< 1.0000, 2.0000, 3.0000>, 2.0000} pigment {color rgbt <0.30, 0.60, 0.90, 0.50>} }",
|
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@s00.to_pov(color: [0.3, 0.6, 0.9], transmit: 0.5) )
|
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20
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end
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end
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22
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@@ -83,37 +88,95 @@ class TC_Povray_Cell < Test::Unit::TestCase
|
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83
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"object { sphere{< 2.0000, 2.0000, 2.0000>, 0.1770} pigment {color rgb <0.53, 0.88, 0.45>} } // Li\n",
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"object { sphere{< 0.4000, 0.6000, 0.8000>, 0.4200} pigment {color rgb <1.00, 0.01, 0.00>} } // O\n",
|
85
90
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]
|
86
|
-
t = @c00.atoms_to_povs(0.01)
|
91
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+
t = @c00.atoms_to_povs(tolerance: 0.01)
|
87
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|
corrects.each_with_index do |correct, index|
|
88
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|
assert_equal(correct, t[index], "line #{index.to_s}")
|
89
94
|
end
|
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95
|
assert_equal(corrects.size, t.size)
|
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|
+
|
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|
+
# with transmit
|
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+
results = @c00.atoms_to_povs(transmit: 0.5)
|
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+
corrects = [ "object { sphere{< 0.0000, 0.0000, 0.0000>, 0.1770} pigment {color rgbt <0.53, 0.88, 0.45, 0.50>} } // Li\n",
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"object { sphere{< 0.4000, 0.6000, 0.8000>, 0.4200} pigment {color rgbt <1.00, 0.01, 0.00, 0.50>} } // O\n"
|
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|
+
]
|
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+
assert_equal(corrects, results)
|
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|
+
|
91
104
|
end
|
92
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-
def
|
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-
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|
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-
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-
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-
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-
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+
def test_bond
|
107
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+
axes = [
|
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|
+
[2.0, 0.0, 0.0],
|
109
|
+
[0.0, 2.0, 0.0],
|
110
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+
[0.0, 0.0, 2.0],
|
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+
]
|
112
|
+
atoms = [
|
113
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+
CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
|
114
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+
CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
|
115
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+
CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
|
116
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+
]
|
117
|
+
c00 = CrystalCell::Povray::Cell.new(axes, atoms)
|
118
|
+
result = c00.bond(['Li1', 'O2'])
|
119
|
+
correct = [
|
120
|
+
"object { cylinder{ < 0.0000, 0.0000, 0.0000>, < 0.3000, 0.3000, 0.4000>, 0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
|
121
|
+
"object { cylinder{ < 0.6000, 0.6000, 0.8000>, < 0.3000, 0.3000, 0.4000>, 0.0500 } pigment { color rgb <1.00, 0.01, 0.00> } }",
|
122
|
+
].join("\n")
|
123
|
+
assert_equal( correct, result)
|
124
|
+
|
125
|
+
result = c00.bond(['Li1-555', 'O2-555'])
|
126
|
+
correct = [
|
127
|
+
"object { cylinder{ < 0.0000, 0.0000, 0.0000>, < 0.3000, 0.3000, 0.4000>, 0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
|
128
|
+
"object { cylinder{ < 0.6000, 0.6000, 0.8000>, < 0.3000, 0.3000, 0.4000>, 0.0500 } pigment { color rgb <1.00, 0.01, 0.00> } }",
|
129
|
+
].join("\n")
|
130
|
+
assert_equal( correct, result)
|
131
|
+
|
132
|
+
result = c00.bond(['Li1-555', 'Li1-556'])
|
133
|
+
correct = [
|
134
|
+
"object { cylinder{ < 0.0000, 0.0000, 0.0000>, < 0.0000, 0.0000, 1.0000>, 0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
|
135
|
+
"object { cylinder{ < 0.0000, 0.0000, 2.0000>, < 0.0000, 0.0000, 1.0000>, 0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
|
136
|
+
].join("\n")
|
137
|
+
assert_equal( correct, result)
|
138
|
+
end
|
139
|
+
|
140
|
+
def test_triangle
|
141
|
+
axes = [
|
142
|
+
[2.0, 0.0, 0.0],
|
143
|
+
[0.0, 2.0, 0.0],
|
144
|
+
[0.0, 0.0, 2.0],
|
145
|
+
]
|
146
|
+
atoms = [
|
147
|
+
CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
|
148
|
+
CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
|
149
|
+
CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
|
150
|
+
]
|
151
|
+
c00 = CrystalCell::Povray::Cell.new(axes, atoms)
|
152
|
+
result = c00.triangle(['Li1', 'O1', 'O2'])
|
153
|
+
correct = [
|
154
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 0.4000, 0.6000, 0.8000>,< 0.6000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
|
155
|
+
].join('')
|
156
|
+
assert_equal( correct, result)
|
157
|
+
end
|
158
|
+
|
159
|
+
def test_tetrahedron
|
160
|
+
axes = [
|
161
|
+
[2.0, 0.0, 0.0],
|
162
|
+
[0.0, 2.0, 0.0],
|
163
|
+
[0.0, 0.0, 2.0],
|
164
|
+
]
|
165
|
+
atoms = [
|
166
|
+
CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
|
167
|
+
CrystalCell::Atom.new("Li", [0.5, 0.5, 0.5]),
|
168
|
+
CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
|
169
|
+
CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
|
170
|
+
]
|
171
|
+
c00 = CrystalCell::Povray::Cell.new(axes, atoms)
|
172
|
+
result = c00.tetrahedron(['Li1', 'Li2', 'O1', 'O2'])
|
173
|
+
correct = [
|
174
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 1.0000>,< 0.4000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
|
175
|
+
"triangle{ < 1.0000, 1.0000, 1.0000>,< 0.4000, 0.6000, 0.8000>,< 0.6000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
|
176
|
+
"triangle{ < 0.4000, 0.6000, 0.8000>,< 0.6000, 0.6000, 0.8000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
|
177
|
+
"triangle{ < 0.6000, 0.6000, 0.8000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 1.0000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}"
|
178
|
+
].join("\n")
|
179
|
+
assert_equal( correct, result)
|
117
180
|
end
|
118
181
|
|
119
182
|
def test_lattice_to_povs
|
@@ -141,7 +204,12 @@ class TC_Povray_Cell < Test::Unit::TestCase
|
|
141
204
|
def test_atom_to_pov
|
142
205
|
assert_equal(
|
143
206
|
"object { sphere{< 0.2000, 0.4000, 0.6000>, 0.1770} pigment {color rgb <0.53, 0.88, 0.45>} } // Li\n",
|
144
|
-
@c00.atom_to_pov( CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]))
|
207
|
+
@c00.atom_to_pov(atom: CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]))
|
208
|
+
)
|
209
|
+
|
210
|
+
assert_equal(
|
211
|
+
"object { sphere{< 0.2000, 0.4000, 0.6000>, 0.1770} pigment {color rgbt <0.53, 0.88, 0.45, 0.50>} } // Li\n",
|
212
|
+
@c00.atom_to_pov(atom: CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]), transmit: 0.5)
|
145
213
|
)
|
146
214
|
end
|
147
215
|
|
@@ -175,5 +243,28 @@ class TC_Povray_Cell < Test::Unit::TestCase
|
|
175
243
|
assert_equal(corrects, t)
|
176
244
|
end
|
177
245
|
|
246
|
+
def test_atom_by_id
|
247
|
+
result = @c00.atom_by_id('Li1-555')
|
248
|
+
correct = CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0])
|
249
|
+
assert_equal(correct, result)
|
250
|
+
|
251
|
+
result = @c00.atom_by_id('Li1-556')
|
252
|
+
correct = CrystalCell::Atom.new("Li", [0.0, 0.0, 1.0])
|
253
|
+
assert_equal(correct, result)
|
254
|
+
|
255
|
+
result = @c00.atom_by_id('Li1-565')
|
256
|
+
correct = CrystalCell::Atom.new("Li", [0.0, 1.0, 0.0])
|
257
|
+
assert_equal(correct, result)
|
258
|
+
|
259
|
+
result = @c00.atom_by_id('Li1-655')
|
260
|
+
correct = CrystalCell::Atom.new("Li", [1.0, 0.0, 0.0])
|
261
|
+
assert_equal(correct, result)
|
262
|
+
|
263
|
+
result = @c00.atom_by_id('Li1-455')
|
264
|
+
correct = CrystalCell::Atom.new("Li", [-1.0, 0.0, 0.0])
|
265
|
+
assert_equal(correct, result)
|
266
|
+
|
267
|
+
end
|
268
|
+
|
178
269
|
end
|
179
270
|
|
@@ -19,10 +19,10 @@ class TC_Tetrahedron < Test::Unit::TestCase
|
|
19
19
|
def test_to_pov
|
20
20
|
#VERTEX_INDICES_OF_TRIANGLES = [ [ 0, 1, 2 ], [ 1, 2, 3 ], [ 2, 3, 0 ], [ 3, 0, 1 ] ]
|
21
21
|
correct = [
|
22
|
-
"triangle{<0.
|
23
|
-
"triangle{<1.
|
24
|
-
"triangle{<0.
|
25
|
-
"triangle{<1.
|
22
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
|
23
|
+
"triangle{ < 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
|
24
|
+
"triangle{ < 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
|
25
|
+
"triangle{ < 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
|
26
26
|
].join("\n")
|
27
27
|
assert_equal(
|
28
28
|
correct,
|
@@ -31,10 +31,10 @@ class TC_Tetrahedron < Test::Unit::TestCase
|
|
31
31
|
|
32
32
|
@t00.transmit = 0.5
|
33
33
|
correct = [
|
34
|
-
"triangle{<0.
|
35
|
-
"triangle{<1.
|
36
|
-
"triangle{<0.
|
37
|
-
"triangle{<1.
|
34
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit 0.5000}}",
|
35
|
+
"triangle{ < 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit 0.5000}}",
|
36
|
+
"triangle{ < 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit 0.5000}}",
|
37
|
+
"triangle{ < 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit 0.5000}}",
|
38
38
|
].join("\n")
|
39
39
|
assert_equal(
|
40
40
|
correct,
|
@@ -25,13 +25,13 @@ class TC_Triangle < Test::Unit::TestCase
|
|
25
25
|
|
26
26
|
def test_to_pov
|
27
27
|
assert_equal(
|
28
|
-
"triangle{<0.
|
28
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 1.0000, 0.0000, 0.0000>,< 0.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
|
29
29
|
@t00.to_pov
|
30
30
|
)
|
31
31
|
|
32
32
|
@t00.transmit = 0.5
|
33
33
|
assert_equal(
|
34
|
-
"triangle{<0.
|
34
|
+
"triangle{ < 0.0000, 0.0000, 0.0000>,< 1.0000, 0.0000, 0.0000>,< 0.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit 0.5000}}",
|
35
35
|
@t00.to_pov
|
36
36
|
)
|
37
37
|
end
|
data/test/test_cell.rb
CHANGED
@@ -3,6 +3,7 @@
|
|
3
3
|
|
4
4
|
require "helper"
|
5
5
|
require 'stringio'
|
6
|
+
require 'pp'
|
6
7
|
|
7
8
|
#class CrystalCell::Cell
|
8
9
|
# public :symmetry_operations
|
@@ -33,8 +34,8 @@ class TC_Cell < Test::Unit::TestCase
|
|
33
34
|
# Li と O を1つずつ入れたセル。
|
34
35
|
# @c02 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] )
|
35
36
|
atoms = [
|
36
|
-
CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
|
37
|
-
CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
|
37
|
+
CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0], 'Li1' ),
|
38
|
+
CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2], 'O1' ),
|
38
39
|
]
|
39
40
|
@c02 = CrystalCell::Cell.new(vectors00, atoms)
|
40
41
|
@c02.comment = 'c02'
|
@@ -214,8 +215,6 @@ class TC_Cell < Test::Unit::TestCase
|
|
214
215
|
assert_in_delta( 0.0, c10.axes[2][0], $tolerance )
|
215
216
|
assert_in_delta( 0.0, c10.axes[2][1], $tolerance )
|
216
217
|
assert_in_delta( 2.0, c10.axes[2][2], $tolerance )
|
217
|
-
|
218
|
-
|
219
218
|
end
|
220
219
|
|
221
220
|
def test_positions
|
@@ -244,6 +243,25 @@ class TC_Cell < Test::Unit::TestCase
|
|
244
243
|
assert_equal( [1, 2], @c04.select_indices{ |i| i.position[0] > 0.05 } )
|
245
244
|
end
|
246
245
|
|
246
|
+
def test_atoms_of_element
|
247
|
+
vectors00 = [[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]
|
248
|
+
atom0 = CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] )
|
249
|
+
atom1 = CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] )
|
250
|
+
atom2 = CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] )
|
251
|
+
atoms = [ atom0, atom1, atom2]
|
252
|
+
c04 = CrystalCell::Cell.new(vectors00, atoms)
|
253
|
+
c04.comment = 'c04'
|
254
|
+
|
255
|
+
assert_equal([atom0, atom1], c04.atoms_of_element('Li'))
|
256
|
+
assert_equal([atom2] , c04.atoms_of_element('O'))
|
257
|
+
assert_equal([] , c04.atoms_of_element('S'))
|
258
|
+
end
|
259
|
+
|
260
|
+
#def test_supercell
|
261
|
+
# @c02.supercell(
|
262
|
+
|
263
|
+
#end
|
264
|
+
|
247
265
|
def test_atoms_in_supercell
|
248
266
|
t = @c02.atoms_in_supercell( 0, 0, 0, 0, 0, 1 )
|
249
267
|
assert_equal( 'Li', t[0].element )
|
@@ -257,61 +275,63 @@ class TC_Cell < Test::Unit::TestCase
|
|
257
275
|
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 1.2], t[3].position )
|
258
276
|
|
259
277
|
t = @c02.atoms_in_supercell(-1, 1,-1, 1,-1, 1 )
|
260
|
-
assert_equal(
|
261
|
-
assert_equal(
|
262
|
-
assert_equal(
|
263
|
-
assert_equal(
|
264
|
-
assert_equal(
|
265
|
-
assert_equal(
|
266
|
-
assert_equal(
|
267
|
-
assert_equal(
|
268
|
-
assert_equal(
|
269
|
-
assert_equal(
|
270
|
-
assert_equal(
|
271
|
-
assert_equal(
|
272
|
-
assert_equal(
|
273
|
-
assert_equal(
|
274
|
-
assert_equal(
|
275
|
-
assert_equal(
|
276
|
-
assert_equal(
|
277
|
-
assert_equal(
|
278
|
-
assert_equal(
|
279
|
-
assert_equal(
|
280
|
-
assert_equal(
|
281
|
-
assert_equal(
|
282
|
-
assert_equal(
|
283
|
-
assert_equal(
|
284
|
-
assert_equal(
|
285
|
-
assert_equal(
|
286
|
-
assert_equal(
|
287
|
-
assert_equal(
|
288
|
-
assert_equal(
|
289
|
-
assert_equal(
|
290
|
-
assert_equal(
|
291
|
-
assert_equal(
|
292
|
-
assert_equal(
|
293
|
-
assert_equal(
|
294
|
-
assert_equal(
|
295
|
-
assert_equal(
|
296
|
-
assert_equal(
|
297
|
-
assert_equal(
|
298
|
-
assert_equal(
|
299
|
-
assert_equal(
|
300
|
-
assert_equal(
|
301
|
-
assert_equal(
|
302
|
-
assert_equal(
|
303
|
-
assert_equal(
|
304
|
-
assert_equal(
|
305
|
-
assert_equal(
|
306
|
-
assert_equal(
|
307
|
-
assert_equal(
|
308
|
-
assert_equal(
|
309
|
-
assert_equal(
|
310
|
-
assert_equal(
|
311
|
-
assert_equal(
|
312
|
-
assert_equal(
|
313
|
-
assert_equal(
|
314
|
-
assert_equal(
|
278
|
+
assert_equal(['Li']*27 + ['O'] * 27 , t.map{|i| i.element} )
|
279
|
+
assert_equal(Mageo::Vector3DInternal[-1.0,-1.0,-1.0],t[ 0].position)
|
280
|
+
assert_equal(Mageo::Vector3DInternal[-1.0,-1.0, 0.0],t[ 1].position)
|
281
|
+
assert_equal(Mageo::Vector3DInternal[-1.0,-1.0, 1.0],t[ 2].position)
|
282
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 0.0,-1.0],t[ 3].position)
|
283
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 0.0, 0.0],t[ 4].position)
|
284
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 0.0, 1.0],t[ 5].position)
|
285
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 1.0,-1.0],t[ 6].position)
|
286
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 1.0, 0.0],t[ 7].position)
|
287
|
+
assert_equal(Mageo::Vector3DInternal[-1.0, 1.0, 1.0],t[ 8].position)
|
288
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0,-1.0],t[ 9].position)
|
289
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0, 0.0],t[10].position)
|
290
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0, 1.0],t[11].position)
|
291
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0,-1.0],t[12].position)
|
292
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0, 0.0],t[13].position)
|
293
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0, 1.0],t[14].position)
|
294
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0,-1.0],t[15].position)
|
295
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0, 0.0],t[16].position)
|
296
|
+
assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0, 1.0],t[17].position)
|
297
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0,-1.0],t[18].position)
|
298
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0, 0.0],t[19].position)
|
299
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0, 1.0],t[20].position)
|
300
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0,-1.0],t[21].position)
|
301
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0, 0.0],t[22].position)
|
302
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0, 1.0],t[23].position)
|
303
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0,-1.0],t[24].position)
|
304
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0, 0.0],t[25].position)
|
305
|
+
assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0, 1.0],t[26].position)
|
306
|
+
assert_equal(Mageo::Vector3DInternal[-0.8,-0.8,-0.8],t[27].position)
|
307
|
+
assert_equal(Mageo::Vector3DInternal[-0.8,-0.8, 0.2],t[28].position)
|
308
|
+
assert_equal(Mageo::Vector3DInternal[-0.8,-0.8, 1.2],t[29].position)
|
309
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 0.2,-0.8],t[30].position)
|
310
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 0.2, 0.2],t[31].position)
|
311
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 0.2, 1.2],t[32].position)
|
312
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 1.2,-0.8],t[33].position)
|
313
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 1.2, 0.2],t[34].position)
|
314
|
+
assert_equal(Mageo::Vector3DInternal[-0.8, 1.2, 1.2],t[35].position)
|
315
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8,-0.8],t[36].position)
|
316
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8, 0.2],t[37].position)
|
317
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8, 1.2],t[38].position)
|
318
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2,-0.8],t[39].position)
|
319
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2, 0.2],t[40].position)
|
320
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2, 1.2],t[41].position)
|
321
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2,-0.8],t[42].position)
|
322
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2, 0.2],t[43].position)
|
323
|
+
assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2, 1.2],t[44].position)
|
324
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8,-0.8],t[45].position)
|
325
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8, 0.2],t[46].position)
|
326
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8, 1.2],t[47].position)
|
327
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2,-0.8],t[48].position)
|
328
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2, 0.2],t[49].position)
|
329
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2, 1.2],t[50].position)
|
330
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2,-0.8],t[51].position)
|
331
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2, 0.2],t[52].position)
|
332
|
+
assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2, 1.2],t[53].position)
|
333
|
+
|
334
|
+
assert_equal('Li1-444',t[ 0].name)
|
315
335
|
end
|
316
336
|
|
317
337
|
def test_elements
|
@@ -968,11 +988,11 @@ class TC_Cell < Test::Unit::TestCase
|
|
968
988
|
# checking atom 0
|
969
989
|
assert_equal( 'Li' , t.atoms[0].element)
|
970
990
|
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
971
|
-
assert_equal(
|
991
|
+
assert_equal( 'Li1' , t.atoms[0].name )
|
972
992
|
# checking atom 1
|
973
993
|
assert_equal( 'O' , t.atoms[1].element)
|
974
994
|
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
975
|
-
assert_equal(
|
995
|
+
assert_equal( 'O1' , t.atoms[1].name )
|
976
996
|
end
|
977
997
|
|
978
998
|
def test_inverse_axis
|
@@ -995,11 +1015,11 @@ class TC_Cell < Test::Unit::TestCase
|
|
995
1015
|
# checking atom 0
|
996
1016
|
assert_equal( 'Li' , t.atoms[0].element)
|
997
1017
|
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
998
|
-
assert_equal(
|
1018
|
+
assert_equal( 'Li1' , t.atoms[0].name )
|
999
1019
|
# checking atom 1
|
1000
1020
|
assert_equal( 'O' , t.atoms[1].element)
|
1001
1021
|
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
1002
|
-
assert_equal(
|
1022
|
+
assert_equal( 'O1' , t.atoms[1].name )
|
1003
1023
|
# checking non-destructive
|
1004
1024
|
assert_equal( CrystalCell::Cell, t.class )
|
1005
1025
|
assert_in_delta( 2.0, @c02.axes[0][0], $tolerance )
|
@@ -1015,11 +1035,11 @@ class TC_Cell < Test::Unit::TestCase
|
|
1015
1035
|
# checking atom 0
|
1016
1036
|
assert_equal( 'Li' , @c02.atoms[0].element)
|
1017
1037
|
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position)
|
1018
|
-
assert_equal(
|
1038
|
+
assert_equal( 'Li1' , @c02.atoms[0].name )
|
1019
1039
|
# checking atom 1
|
1020
1040
|
assert_equal( 'O' , @c02.atoms[1].element)
|
1021
1041
|
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], @c02.atoms[1].position)
|
1022
|
-
assert_equal(
|
1042
|
+
assert_equal( 'O1' , @c02.atoms[1].name )
|
1023
1043
|
|
1024
1044
|
# y 軸反転
|
1025
1045
|
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
@@ -1043,11 +1063,11 @@ class TC_Cell < Test::Unit::TestCase
|
|
1043
1063
|
# checking atom 0
|
1044
1064
|
assert_equal( 'Li' , t.atoms[0].element)
|
1045
1065
|
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
1046
|
-
assert_equal(
|
1066
|
+
assert_equal( 'Li1' , t.atoms[0].name )
|
1047
1067
|
# checking atom 1
|
1048
1068
|
assert_equal( 'O' , t.atoms[1].element)
|
1049
1069
|
assert_equal( Mageo::Vector3DInternal[ 0.2,-0.2, 0.2], t.atoms[1].position)
|
1050
|
-
assert_equal(
|
1070
|
+
assert_equal( 'O1' , t.atoms[1].name )
|
1051
1071
|
|
1052
1072
|
# z 軸反転
|
1053
1073
|
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
@@ -1072,11 +1092,11 @@ class TC_Cell < Test::Unit::TestCase
|
|
1072
1092
|
# checking atom 0
|
1073
1093
|
assert_equal( 'Li' , t.atoms[0].element)
|
1074
1094
|
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
1075
|
-
assert_equal(
|
1095
|
+
assert_equal( 'Li1' , t.atoms[0].name )
|
1076
1096
|
# checking atom 1
|
1077
1097
|
assert_equal( 'O' , t.atoms[1].element)
|
1078
1098
|
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2,-0.2], t.atoms[1].position)
|
1079
|
-
assert_equal(
|
1099
|
+
assert_equal( 'O1' , t.atoms[1].name )
|
1080
1100
|
|
1081
1101
|
end
|
1082
1102
|
|
@@ -1102,7 +1122,7 @@ class TC_Cell < Test::Unit::TestCase
|
|
1102
1122
|
# checking atom 1
|
1103
1123
|
assert_equal( 'O' , t.atoms[1].element)
|
1104
1124
|
assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
|
1105
|
-
assert_equal( nil
|
1125
|
+
assert_equal( nil , t.atoms[1].name )
|
1106
1126
|
end
|
1107
1127
|
|
1108
1128
|
def test_exchange_axes
|
@@ -1285,7 +1305,6 @@ class TC_Cell < Test::Unit::TestCase
|
|
1285
1305
|
end
|
1286
1306
|
|
1287
1307
|
def test_symmetry_operations
|
1288
|
-
f13 = 1.0/3.0
|
1289
1308
|
|
1290
1309
|
#cubic/POSCAR #Pm-3m (221) / m-3m / -P 4 2 3 (517)
|
1291
1310
|
corrects = [
|
@@ -1416,6 +1435,7 @@ class TC_Cell < Test::Unit::TestCase
|
|
1416
1435
|
#]
|
1417
1436
|
#assert_equal(corrects, @c15 .symmetry_operations) #triclinic
|
1418
1437
|
|
1438
|
+
#f13 = 1.0/3.0
|
1419
1439
|
##trigonal/POSCAR #P-3m1 (164) / -3m / -P 3 2= (456)
|
1420
1440
|
#corrects = [
|
1421
1441
|
# {:rotation => [[ 1.0, 0.0, 0], [ 0.0, 1.0, 0], [ 0.0, 0.0, 1.0]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: crystalcell
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- ippei94da
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2017-05-23 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: test-unit
|