Dear lammps users,
Sorry for the basic question, I am trying to analyze the results of Hydrocarbon MD simulation. As a simple tutorial, I am running ‘CH4 + OH’ simulation with these command lines
‘fix 4 all reax/c/bonds 10 bonds.tatb’
‘fix 5 all reax/c/species 1 10 10 reax_species.out element C H O cutoff 1 1 0.5 cutoff 1 2 0.5 cutoff 1 3 0.5 cutoff 2 2 0.5 cutoff 2 3 0.5 cutoff 3 3 0.5’
When I analyze the results ‘reax_species.out’ file, I find strange species ‘CH2’&’H’ at Timestep 450. How does the command(reax/c/species) classify the molecule(species)? Isn’t this command classifying species using bond-order cutoff value? When I check the bond-order at Timestep 450 through the ‘bonds.tatb’ file, I can’t find the reason why the species of ‘CH2’ and ‘H’ were generated.
The output file (reax_species.out and bonds.tatb)are attached. Any advice is very much appreciated.
Best regards,
jongwun
reax_species.out
Timestep No_Moles No_Specs CH3 H2O
400 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
410 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
420 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
430 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
440 2 2 1 1
Timestep No_Moles No_Specs CH2 H2O H
450 3 3 1 1 1
Timestep No_Moles No_Specs CH3 H2O
460 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
470 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
480 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
490 2 2 1 1
Timestep No_Moles No_Specs CH3 H2O
500 2 2 1 1
bonds.tatb
Timestep 400
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.966 0.962 0.903 2.922 0.006 -0.285
2 2 1 6 0 0.962 1.045 0.000 0.456
3 2 1 1 0 0.966 0.976 0.000 0.041
4 2 1 1 0 0.962 0.970 0.000 0.085
5 2 1 1 0 0.903 0.907 0.000 0.078
6 3 2 2 7 0 0.962 0.920 1.898 2.000 -0.648
7 2 1 6 0 0.920 0.927 0.000 0.273
Timestep 410
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.962 0.969 0.944 2.896 0.008 -0.289
2 2 1 6 0 0.964 0.982 0.000 0.438
3 2 1 1 0 0.962 0.974 0.000 0.038
4 2 1 1 0 0.969 0.977 0.000 0.092
5 2 1 1 0 0.944 0.951 0.000 0.098
6 3 2 2 7 0 0.964 0.876 1.855 2.000 -0.586
7 2 1 6 0 0.876 0.887 0.000 0.209
Timestep 420
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.958 0.972 0.974 2.925 0.005 -0.300
2 2 1 6 0 0.946 0.967 0.000 0.376
3 2 1 1 0 0.958 0.969 0.000 0.036
4 2 1 1 0 0.972 0.980 0.000 0.099
5 2 1 1 0 0.974 0.984 0.000 0.124
6 3 2 2 7 0 0.946 0.823 1.782 2.000 -0.504
7 2 1 6 0 0.823 0.836 0.000 0.169
Timestep 430
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.953 0.971 0.987 2.979 0.003 -0.311
2 2 1 6 0 0.901 0.969 0.000 0.302
3 2 1 1 0 0.953 0.963 0.000 0.035
4 2 1 1 0 0.971 0.979 0.000 0.102
5 2 1 1 0 0.987 0.998 0.000 0.149
6 3 2 2 7 0 0.901 0.789 1.700 2.000 -0.433
7 2 1 6 0 0.789 0.800 0.000 0.156
Timestep 440
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.951 0.966 0.989 3.213 0.000 -0.303
2 2 1 6 0 0.828 1.135 0.000 0.241
3 2 1 1 0 0.951 0.959 0.000 0.035
4 2 1 1 0 0.966 0.974 0.000 0.098
5 2 1 1 0 0.989 1.001 0.000 0.156
6 3 2 2 7 0 0.828 0.793 1.629 2.000 -0.391
7 2 1 6 0 0.793 0.802 0.000 0.163
Timestep 450
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.951 0.959 0.985 3.008 0.002 -0.264
2 2 1 6 0 0.773 0.890 0.000 0.197
3 2 1 1 0 0.951 0.958 0.000 0.036
4 2 1 1 0 0.959 0.966 0.000 0.087
5 2 1 1 0 0.985 0.995 0.000 0.140
6 3 2 2 7 0 0.773 0.841 1.621 2.000 -0.383
7 2 1 6 0 0.841 0.853 0.000 0.187
Timestep 460
Number of particles 7
Max number of bonds per atom 4 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 4 2 3 4 5 0 0.444 0.954 0.951 0.969 3.325 0.000 -0.226
2 2 2 1 6 0 0.444 0.703 1.156 0.000 0.168
3 2 1 1 0 0.954 0.959 0.000 0.034
4 2 1 1 0 0.951 0.955 0.000 0.076
5 2 1 1 0 0.969 0.974 0.000 0.115
6 3 2 2 7 0 0.703 0.895 1.605 2.000 -0.399
7 2 1 6 0 0.895 0.901 0.000 0.231
Timestep 470
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.959 0.947 0.935 3.045 0.001 -0.195
2 2 1 6 0 0.698 0.905 0.000 0.151
3 2 1 1 0 0.959 0.963 0.000 0.034
4 2 1 1 0 0.947 0.949 0.000 0.067
5 2 1 1 0 0.935 0.937 0.000 0.094
6 3 2 2 7 0 0.698 0.940 1.644 2.000 -0.441
7 2 1 6 0 0.940 0.946 0.000 0.290
Timestep 480
Number of particles 7
Max number of bonds per atom 4 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 4 2 3 4 5 0 0.391 0.962 0.947 0.892 3.199 0.000 -0.188
2 2 2 1 6 0 0.391 0.703 1.101 0.000 0.160
3 2 1 1 0 0.962 0.967 0.000 0.030
4 2 1 1 0 0.947 0.949 0.000 0.063
5 2 1 1 0 0.892 0.893 0.000 0.083
6 3 2 2 7 0 0.703 0.960 1.669 2.000 -0.488
7 2 1 6 0 0.960 0.963 0.000 0.339
Timestep 490
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.964 0.954 0.873 2.970 0.003 -0.193
2 2 1 6 0 0.760 0.940 0.000 0.193
3 2 1 1 0 0.964 0.968 0.000 0.025
4 2 1 1 0 0.954 0.955 0.000 0.065
5 2 1 1 0 0.873 0.874 0.000 0.079
6 3 2 2 7 0 0.760 0.962 1.728 2.000 -0.517
7 2 1 6 0 0.962 0.965 0.000 0.348
Timestep 500
Number of particles 7
Max number of bonds per atom 3 with coarse bond order cutoff 0.300
Particle connection table and bond orders
id type nb id_1…id_nb mol bo_1…bo_nb abo nlp q
1 1 3 3 4 5 0 0.964 0.961 0.892 3.045 0.001 -0.216
2 2 1 6 0 0.818 1.046 0.000 0.246
3 2 1 1 0 0.964 0.968 0.000 0.023
4 2 1 1 0 0.961 0.963 0.000 0.073
5 2 1 1 0 0.892 0.893 0.000 0.080
6 3 2 2 7 0 0.818 0.944 1.767 2.000 -0.519
7 2 1 6 0 0.944 0.946 0.000 0.312
