I do not know how to convert the CHARGE format data file to FULL format data file, i.e., how do I add necessary information like bonds, angIes, and etc. to the data file?
I used the ReaxFF potential to describe the pyrolysis processes, and then I can get a data file (CHARGE format) from the pyrolysis simulation results. Subsequently I would like to simulate the mechanical loading of the structure obtained after pyrolysis by classic force fields like PCFF, which needs FULL type data file.
You have to use some external tool for that. There are more steps needed, you also need to identify and assign atom types (in ReaxFF parameters are per element, in PCFF you have multiple atom types for each element depending on the environment) and partial charges consistent with the force field (i.e. not ReaxFF). The bond topology, you can probably import from fix reaxff/bonds, but you also need to derive angle and dihedral topology (this is typically done from the bond topology, check the PCFF publication(s) for details on that). The types for bonded interactions are also usually determined by the atom types, but there may be wildcards in use. Some of these steps can be scripted, some need to be done manually.
I personally would implement this with VMD using its Tcl script interface and various VMD plugins available for some of the steps (including TopoTools), but I am biased, since I wrote TopoTools and know VMD scripting very well, so it is easy for me.
I can convert the .xyz dump file from ReaxFF calculations into a data file with bond information via the TopoTools (topo writelammpsdata data.mysystem full), but the information on angles, dihedrals, and impropers is missing, as shown below:
6557 atoms
7358 bonds
0 angles
0 dihedrals
0 impropers
4 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
…
Also, the molecule information is incorrect.
I would like to add the remaining information via VMD, but I do not have much of a clue right now, do you have a tutorial on this?
Only for parts of the task. Check out the TopoTools documentation.
As I already mentioned, doing this process requires a good understanding of the PCFF force field and that starts with the atom typing. I also mentioned that you can extract the bond/molecule information from LAMMPS with the corresponding fix commands.
You could also leverage this example using Moltemplate. In your case, you only need to assign atom types, charges, and a list of bonds for each unique molecular types in your system. Then you could render the sample with the new force field and the Cartesian coordinates from the old data file.