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, N_H, N_O, O or OH terninated,

if the last number is 2, there must be one OH group. e.g. (1212: CHOH) if the last number is 1, there must be one terminated O. e.g. (1211: CH2O) 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) during calculation,

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 -> C-O + H -> R-C + O + H -> R-C + OH  Vs    R-C-O-H ->  R-C + OH 

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.