Editing Entropy.py

go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[Scripts for VASP]] or [[VASP]]

   [[Image:Get mag.tgz]] 

This script will do the following:

Reads OUTCAR and calculate the entropy contributions of vibrations at desired temperature;


'''Note 1: '''

To get the vibration information, we need set:


 IBRION = 5 
 POTIM  = 0.02 (or smaller 0.01) 
 NSW = 1 
 NFREE = 2 

'''Note 2: '''

For gas and some surface adsorbates, we will get some imaginary frequencies. 
In this script, you can choose to conclude these imaginary frequencies or not. 

'''To use this script:'''

1) make sure that OUTCAR is in the path when you run this script. 

   
2) Use the command below: 

    python entropy-v4-2.py Temperature 


3) Choose to consider imaginary frequencies or not.


Enjoy!


----

 # -*- coding: utf-8 -*-
 #!/usr/bin/env python 
 # Version-4.2: Changed the Reminder from Gas into Imaginary frequencies.
 # -*- coding: utf-8 -*-
 # Writen By Qiang Li from ICIQ in 23-09-2017
 # Ref: Atkin's Physical chemistry, 10th Edition, Statistical thermodynamics: the vibrational Contribution, Page: 642
 # To use it: python entropy-v4.py 273.15  (273.15 is the Temperature!!!)
 # Then choose the calculation type by follow the suggestion: Gas calculation or others 
 
 import sys
 import math 
 from scipy import constants as con
 
 script, Tem = sys.argv
 h_p = con.h   # 6.62606957E-34 # J*s Plank Constant
 k_b = con.k   # 1.38064852E-23 # m²*kg*s⁻²*K⁻¹ Boltzman Constant 
 R_gas = con.R # 8.3144598      # J*mol⁻¹*K⁻¹ Gas Constant 
 l_s = con.c   # 299792458      # light speed m * s ⁻¹
 
 Tem = float(Tem)  # Temperature 
 beta = 1/(k_b * Tem)
 
 def get_pf(miu): # get partition function
     x_i = h_p * float(miu) * l_s * beta
     pf_l  = x_i / (math.exp(x_i) -1)   # Lleft part of the partition fuction
     pf_r  = math.log(1-math.exp(-x_i)) 
     pf    = pf_l - pf_r 
     return pf 
 
 look_up1 = 'cm-1'
 look_up2 = 'f/i'
 miu_list = []
 
 status = raw_input('\nDo you want to consider the imaginary frequencies? 1: Yes. 2 No.: Please type 1 or 2\n>>>>\t')
 
 def miu(status):
     with open('OUTCAR') as data_in:
         if status in ['1', 1, 'Yes', 'Y', 'y', 'yes']:  
             for i in data_in.readlines():
                 if look_up1 in i.rstrip() and look_up2 not in i.rstrip():
                     miu_list.append(float(i.split()[7]))
                 elif look_up2  in i.rstrip():
                     miu_list.append(float(i.split()[6]))
         elif status in  ['2', 2, 'No', 'N', 'n', 'no']: 
             for i in data_in.readlines():
                 if look_up1 in i.rstrip() and look_up2 not in i.rstrip():
                     miu_list.append(float(i.split()[7]))                
         else: 
             print "\nPlease Run it again and Type: 1 or 2 !!!\n"
 miu(status)
 miu_list= list(set(miu_list))
 
 sum_pf =  R_gas * sum(get_pf(i*100) for i in miu_list) # Calculate the Entropy S 
 
 TS= Tem * sum_pf  # entropy contribution: T * S 
 
 print 'S in J * K⁻¹ * mol⁻¹:\t%s' %(sum_pf)
 print 'S in eV * K⁻¹ * mol⁻¹:\t%s' %(sum_pf/1000/96.4869)
 print 'T*S in eV * mol⁻¹:\t%s' %(TS/1000/96.4869)