Can ReacNetGenerator process my trajectory?#
Generally ReacNetGenerator has no limitation on any specific elements.
When perceiving bond orders from atomic coordinates, ReacNetGenerator will call Open Babel which reads element parameters.[OBoyleBJ+11] The parameters may not fit the system. If you have new ideas about parameters, you can report to Open Babel and recompile Open Babel from the new source code.
When processing a ReaxFF bond file, bond orders are directly provided by ReaxFF with decimal rounding.[AFPG12] The accuracy of the bond orders depends on the accuracy of the force field.
You can refer the list of publications driven by ReacNetGenerator to see other researchers’ applications.
Out of memory (OOM)#
When processing a large trajectory, you may get different OOM errors such as
Memory Error, or subprocesses are directly killed by the system with
broken pipe thrown. If you have a machine that has more memory, just use it. Otherwise, try to reduce the size of the trajectory or split the trajectory into multiple files or increase the number given by
--stepinterval. It is also helpful to recuding the number of processes.
If you are using a Windows OS, it’s known that the program may consume large memory through multiprocessing. In this situation, it’s suggested to use Windows Subsystem Linux (WSL).