mathjax-yard 0.1.0 → 1.0.1

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Files changed (34) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -1
  3. data/.yardopts +1 -1
  4. data/Rakefile +1 -0
  5. data/doc/MathJaxYard.html +141 -0
  6. data/doc/MathJaxYard/Command.html +1017 -0
  7. data/doc/_index.html +149 -0
  8. data/doc/class_list.html +58 -0
  9. data/doc/css/common.css +1 -0
  10. data/doc/css/full_list.css +57 -0
  11. data/doc/css/style.css +339 -0
  12. data/doc/file.Home.html +86 -0
  13. data/doc/file.README.html +144 -0
  14. data/doc/file.README_ja.html +162 -0
  15. data/doc/file.atom.html +211 -0
  16. data/doc/file.potential2.html +196 -0
  17. data/doc/file_list.html +72 -0
  18. data/doc/frames.html +26 -0
  19. data/doc/index.html +144 -0
  20. data/doc/js/app.js +219 -0
  21. data/doc/js/full_list.js +181 -0
  22. data/doc/js/jquery.js +4 -0
  23. data/doc/method_list.html +129 -0
  24. data/doc/top-level-namespace.html +158 -0
  25. data/lib/mathjax-yard.rb +48 -61
  26. data/lib/mathjax-yard/script.rb +20 -0
  27. data/lib/mathjax-yard/version.rb +1 -1
  28. data/mathjax-yard.gemspec +3 -1
  29. data/mathjax.yml +3 -3
  30. data/mathjax.yml.bk +28 -0
  31. metadata +40 -7
  32. data/docs/README_ja.md +0 -77
  33. data/docs/atom.md +0 -121
  34. data/docs/potential2.md +0 -103
data/docs/potential2.md DELETED
@@ -1,103 +0,0 @@
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- # lj0
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- 標準的なLennard-Jonesポテンシャルの表式
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-
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- $$ F(s)=\int_{0}^{\infty}f(t)e^{-st}dt $$
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-
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- ```
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- bob% cat POTCAR
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- ---
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- :type: lj0
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- :element: Al
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- :a0: 1.587401051*0.7071067812/2.857701314;
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- :e0: -1*4.0/12.0;
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- :a: 18.19007708
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- :b: 89.22765864
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- :p: 3.0
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- :q: 5.0
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- :cut_off: 4.0*0.8
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- :energy: -a*(1/r**p)+b*(1/r**q)
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- :dedr: (p*a/r**(p+1.0))-(q*b/r**(q+1.0))
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- ```
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- # lj_jindo
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- 神藤先生あるいはVu Van Huangが使っていたLennard-Jonesポテンシャルの表式．
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- ```ruby
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- bob% cat POTCAR_jindo_Cu
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- ---
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- :type: lj_jindo
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- :element: Cu
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- :d0: 4125.70
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- :n: 9.00
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- :m: 5.50
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- :r0: 2.5487e-8
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- :alat: 3.6153e-8
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- :atom_mass: 63.5460/6.023e23
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- :energy: d0*((r/r0)^(-n)*m-(r/r0)^(-m)*n)/(m-n)
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- :dedr: d0*m*n*((r/r0)^(-m)-(r/r0)^(-n))/(r*(m-n))
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- ```
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- ```
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- Cu
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- d0 := 4125.70;
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- vn := 9.00;
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- vm := 5.50;
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- r0 := 2.5487e-8;
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- rh:=r0/rr;
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- dedr:=unapply(-d0*vm*vn / ((vn-vm)*rr) * (rh**vn - rh**vm),rr);
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- eq1:=int(dedr(r),r);
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- func:=unapply(eq1,rr);
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- r1:=2.5487*10^(-8)*0.8;
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- r2:=2.5487*10^(-8)*1.5;
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- plot(8.617385e-05*func(r),r=r1..r2);
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- ```
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- ```ruby
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- dedr:=unapply(-d0*vm*vn / ((vn-vm)*rr) * (rh**vn - rh**vm),rr);
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- eq1:=int(dedr(r),r);
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- -{ 1.821482757\times 10^{-38}} r{-5.5}+
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- { 2.942122564\times 10^{-65}} r^{-9}
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- ```
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- ```ruby
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- rh:=r0/rr;
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- dedr:=normal(expand(d0*vm*vn / ((vn-vm)*rr) * (rh**vn - rh**vm)));
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- eq1:=simplify(int(dedr,rr));
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- ```
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-
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- $$
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-
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- r_1=r/r_0
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-
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- \frac{ d_0 \left( r_1^{-n}m- r_1^{-m} n \right) }{ -n + m }
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- $$
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-
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- # ポテンシャル選択機構
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- module LJに記述
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- ```ruby
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- def select(file='POTCAR')
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- # p src = YAML.load_file(ARGV[0])
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- p src = YAML.load_file(file)
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- @@potential=case src[:type]
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- when 'lj0'
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- LJ0.new(src)
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- when 'lj_jindo'
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- LJ_Jindo.new(src)
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- end
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- end
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- ```
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- - 委譲による選択
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- - pseudovasp.rbにLJ.select('POTCAR')がある．
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- - LJ0あるいはLJ_Jindoをclassとして用意．
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- - POTCARへのYAMLでの記述
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- - クラス変数によるクラス共通の変数定義
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-
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- EAMとの統一を考えたが，energy, forceのmethodの選択を
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- どっかでしないとダメで，その綺麗なやり方が思いつかず，
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- そのままにした．
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-
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- ```ruby
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- class EAMAtom < Atom
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- include EAM
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- end
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-
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- class LJAtom < Atom
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- include LJ
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- end
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- ```
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- となっており，ほぼ元どおり．