Structure

1. Getting Start：

   

   基础案例：

   # Typical script
   #Load the TAMkin package
   from tamkin import *
   
   #Load the data
   molecule = load_molecule_g03fchk("gaussian.fchk")
   #Perform normal mode analysis:
   #If the second argument is omitted, the frequency computation is performed in 3N degrees of freedom. The ConstrainExt() variant will perform the normal mode analysis in 3N-6 (or 3N-5) internal coordinates and leads to frequencies that are identical to those of Gaussian.
   nma = NMA(molecule, ConstrainExt())
   #Construct a partition function
   #A PartFun object is a definition of the partion function. All thermodynamic quantities are methods or attributes of the PartFun object. The translational and rotational contributions are included by adding [ExtTrans(), ExtRot()] as an argument. The vibrational and electronic contribution is included implicitely.
   pf = PartFun(nma, [ExtTrans(), ExtRot()])
   
   # Write some general information about the molecule
   # and the partition function to a file.
   pf.write_to_file("partfun.txt")
   
   # Write an extensive overview of the thermodynamic properties to a file:
   ta = ThermoAnalysis(pf, [300,400,500,600])
   ta.write_to_file("thermo.csv")
   

2. Tamkin可以读取哪些数据：

   • CHARMM：输入文件需要含有VIBRAN部分

     CALC k = 3 * ?NATOM
     VIBRan NMODes @k
     OPEN WRITe CARD UNIT 20 NAME filename.hessian
     WRITe SECOnd CARD UNIT 20
     * title - Full Hessian
     *
     END
     

   • CP2K:

     • The optimization:

       &GLOBAL
         RUN_TYPE GEO_OPT
         PRINT_LEVEL LOW
       &END GLOBAL
       

     • The calculation of the energy (one SCF optimization):

       &GLOBAL
         RUN_TYPE  ENERGY_FORCE
         PRINT_LEVEL HIGH
       &END GLOBAL
       

     • The frequency calculation:

       Gaussian 98/03/09&VIBRATIONAL_ANALYSIS
         FULLY_PERIODIC T
       &END VIBRATIONAL_ANALYSIS
       ...
       &MOTION
          # Optionally constrain some atoms, such that only a partial Hessian is
          # computed. The same constraints can be used in the optimization.
          # You should not use _more_ constraints in the optimization. Less is OK but
          # sometimes not needed.
          &CONSTRAINT
             &FIXED_ATOMS
                 COMPONENTS_TO_FIX  XYZ
                 LIST {integer}  or a range {integer}..{integer}
             &END FIXED_ATOMS
          &END CONSTRAINT
       &END MOTION
       ...
       &GLOBAL
         RUN_TYPE  vibrational_analysis
         PRINT_LEVEL medium
       &END GLOBAL
       

   • Gaussian 98/03/09：

     • 保持checkpoint file：%chk=prefix.chk
     • 计算完成后：formchk prefix.chk prefix.fchk

3. 理论背景：http://molmod.github.io/tamkin/tutorial/chemphys_theory.html