Editing Version-6.py

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[[Image:version-6.tgz]]

This Script Generates Glycerol Decomposition Network and Complete Intermediates 


'''How to use it :  python version-6.py'''

'''The 1st File Generated: species_list.txt :''' 

 ''Lables,            Structures,   Formula, Number_H, Number_O''
 ''1312-1212-1312,HOCH2-CHOH-CH2OH,  C3H8O3,    8,        3 ''

'''Note:'''   1312 stands for HOCH2(on left) and CH2OH (on right) :  N_C(1), N_H(3), N_O(1),  O or OH terninated(2), 

if the last number is 2, there must be one OH group. e.g. (1212: CHOH or HOCH)

if the last number is 1, there must be one terminated O. e.g. (1211: CH2O or OCH2)

if the last two numbers are 00, there is no O or OH. e.g. (1200, CH2)

'''The 2nd File Generated: reaction_list.txt:''' 

 ''Lables(IS),     Structures(IS),   Lables(FS1),      Structures(FS1),   Lables(FS2), Structures(FS2), Bond_Type, Formula(IS), Formula(FS) ''
 ''1312-1212-1312, HOCH2-CHOH-CH2OH, 1212-1312:1312,  HOCH-CH2OH:CH2OH,       1312,         CH2OH,           C-C,      C3H8O3,     C2H5O2 ''

'''Note:'''  ':' in 1212-1312:1312 means that C--C bond breaks 
'''
The 3rd File Generated: label_dic.txt, c1c2c3.txt ''(By hand)'''''

Each specie is given a name (Number label) for  calculation convenience purpose. 

'''Example1:'''  Glycerol (831) the first structure which has 8 H and 3 O atoms. 

'''Example2:'''  If there are four isomers with formula of C3H7O3, then they are named as 731, 732, 733, and 734. 

After Finishing 269 structures' geometry calculation, add their energies to species_list.txt, and we get label_dic.txt

  ''Lables,         Structures,       Formula, Number_H, Number_O, Number label, E_No_ZPVE,        E_ZPVE ''
  ''1312-1212-1312, HOCH2-CHOH-CH2OH, C3H8O3,     8,        3,        831,       -394.75896253,  -391.648156448''
 
c1c2c3.txt contains C1, C2, and C3 species' energies. 

  ''Lables,          E_No_ZPVE,     E_ZPVE''
  ''1312-1212-1312,-394.75896253,-391.648156448''
'''
The 4th File Generated: reaction_energy.txt'''

  ''E_OH, E_H, E_slab, E_glycerol(gas) are used as reference energies.''

  '' Lable(IS),    Lable(FS1),      Label(FS2), Bond_Type,  E_IS,          E_FS,          E_TS,        Ea,           Delta_E,   E_IS(abs),    E_FS(abs)
  ''1312-1212-1312,1212-1312:1312,    1312,     C-C,       -1.081190489,-1.008524381,0.135859216145,1.21704970515,0.072666108,-1.081190489,-1.008524381

'''Note1:'''  E_IS, E_FS, and E_TS are calculated with reference energies based on IS. 

'''Note2:'''  E_IS(abs), E_FS(abs) are calculated with reference energies based on IS and FS1, separately.

'''Diferences:''' The differences between these two energies mainly focus on some reactions correlated with C--OH bond breaking or C--O bond breaking. 

  ''R-C-O-H -> RC-O + H -> R-C(1) + O + H -> R-C  + OH''  '''Vs'''   '' R-C-O-H ->  R-C(2) + OH ''

  ''R-C(1) and R-C(2) have different referenced energy. The difference is reaction energy of O + H -> OH on the surface.   ''

'''
The 5th File Generated: selected_reactions.txt'''

'''Choose Reactions:'''

   '''Rule-1:'''  The C--H breaking from the second C (1212, 1111) is impossible as the H is in the gas phase. 

   '''Rule-2'''   From one specie, select the reaction with lowest barrier.  if the barrier from another reaction is 0.30 eV high than the lowest, delete the reaction 

'''The 6th File Generated: filtered_reactions.txt'''

  '''Rule-3:'''  Some reactions can not happen because it can not produced from previous reaction. Remove these reactions.


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'''Plotting Energy Profile'''