Hello:
I have interest in using ReaxFF potential to simulation oxidation in SiC. Oxygen molecules will be deposited in the vacuum above SiC bulk. Well, I have a problem in using fix deposit molecule command within lammps.
In my simulation, firstly, read_data is used to read in the substrate Si and C atoms coordinates, which included the “1 extra bond per atom” to leave space to add molecules.Then, O2 molecular file is read, which includes atom coordinates, atom types, and bonds information. This is a simplified version from the lammps/example/deposit/molecule, which includes special bond information. Lastly, fix deposit command is used. Input files have been attached.
However, I continuously get the error messages: ERROR: Molecule topology type exceeds system topology type (../molecule.cpp:1368). I have checked the create_box command instruction. As I used read_data which is an equal command of create_box, and "1 extra bond per atom” is included. I don’t know are there thing wrong with my read_data or O2.txt file.
Could you give me some suggestions on using read_data, reaxff potential and fix_deposit properly?
Thanks in advance!
Cheng
in.32fast (2.64 KB)
O2.txt (124 Bytes)
011_Bulk_Readin.txt (520 KB)
Hello:
I have interest in using ReaxFF potential to simulation oxidation in SiC. Oxygen molecules will be deposited in the vacuum above SiC bulk. Well, I have a problem in using fix deposit molecule command within lammps.
In my simulation, firstly, read_data is used to read in the substrate Si and C atoms coordinates, which included the “1 extra bond per atom” to leave space to add molecules.Then, O2 molecular file is read, which includes atom coordinates, atom types, and bonds information. This is a simplified version from the lammps/example/deposit/molecule, which includes special bond information. Lastly, fix deposit command is used. Input files have been attached.
However, I continuously get the error messages: ERROR: Molecule topology type exceeds system topology type (../molecule.cpp:1368). I have checked the create_box command instruction. As I used read_data which is an equal command of create_box, and "1 extra bond per atom” is included. I don’t know are there thing wrong with my read_data or O2.txt file.
Could you give me some suggestions on using read_data, reaxff potential and fix_deposit properly?
in reaxff there should be no explicit bonds given anywhere, since
bondorder and its derived interactions are computed dynamically during
the simulation.
axel.