Linux基本重要操作指令:

  cd變換目錄, pwd(PrintWorkingDirectory)顯示當下路徑,

  mkdir/rmdir(MakeDirectory/RemoveDirectory)建立/刪除目錄, ls顯示檔案名稱, cp(copy)複製貼上,

  rm(remove)刪除檔案, rm -rf (re force)強制刪除資料夾, mv (move) 移動,

  less觀看檔案內容, vi文書處理 --> i編輯 --> esc一般模式 --> :wq儲存離開, :q!離開不儲存

座標建立:

     1. 直角座標

     2. 分子內部座標

     ex: CH₄                   

         1 C

         2 H 1 R

         3 H 1 R 2 A

         4 H 1 R 2 A 3 D

         5 H 1 R 2 A 3 -D

           R=1.07

           A=109.47122

           D=120  

     ex: C₂H₄

         1 C                      

         2 C 1 R1

         3 H 1 R2 2 A1

         4 H 1 R2 2 A1 3 180

         5 H 2 R2 1 A1 3 180

         6 H 2 R2 1 A1 3 0   

Single Point Energy Calculation:

     ex: #T RHF/6-31G(d) Pop=Full Test      

                    #T: request terse output from program

  method    HF: 使用 Hartree-Fock 理論，也就是用一個行列式 (slater determinant) 來代表波函數

         (mp2, mp3 ...)

         R: restricted (U: unrestricted)

  basis         6-31G(d): 這K個AO就稱為計算使用之基底函數 (basis functions or basis set)

  job         Pop=Full

        最後求得能量、分子軌域、軌域能量、Charges、Dipole 和 Multipole moments…等

       ex: Propene Single Point (#T RHF/6-31G(d) Test)

             Hartree-Fock energy: SCF Done: E(RHF) = -117.065692097 A.U. after 5 cycles

               Mulliken atomic charges:
              1
              1 C -0.388759
              2 C -0.156384
              3 C -0.507949
              4 H 0.170153
              5 H 0.173467
              6 H 0.184153
              7 H 0.165601
              8 H 0.179859
              9 H 0.179859
              Sum of Mulliken charges= 0.00000

              Dipole moment (field-independent basis, Debye):
              X= -0.3030 Y= -0.0298 Z= 0.0000 Tot= 0.3045

Geometry Optimization:

     Optimization的目的是為了找出PES的min =>  Convergence Criteria  => 求得最佳化結構

     ex: #T RHF/6-31G(d) Opt Test

       Vinyl Alcohol CCOH=0                          Vinyl Alcohol CCOH=180                                   Acetaldehyde

    Vinyl Alcohol CCOH=0 Geom. Opt.
        SCF Done: E(RHF) = -152.888886562 A.U. after 8 cycles

        Vinyl Alcohol CCOH=180 Geom. Opt.
        SCF Done: E(RHF) = -152.885388871 A.U. after 10 cycles

        Acetaldehyde Geom. Opt.
        SCF Done: E(RHF) = -152.915965413 A.U. after 8 cycles

     變換 basis set 及不同方法求相同的分子, 看其與實驗數據的差別, 還有計算上的效率

     (MNDO, PM3, HF/STO-3G, HF/3-21G)

      Reactant => Product 之間的 Transition Structure 最佳化