Version-6.py

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File: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