dpgen init_reaction parameters

init_reaction_jdata:

type: dict

argument path: init_reaction_jdata

Generate initial data for reactive systems for small gas-phase molecules, from a ReaxFF NVT MD trajectory.

type_map:

type: list

argument path: init_reaction_jdata/type_map

Type map, which should match types in the initial data. e.g. [“C”, “H”, “O”]

reaxff:

type: dict

argument path: init_reaction_jdata/reaxff

Parameters for ReaxFF NVT MD.

data:

type: str

argument path: init_reaction_jdata/reaxff/data

Path to initial LAMMPS data file. The atom_style should be charge.

ff:

type: str

argument path: init_reaction_jdata/reaxff/ff

Path to ReaxFF force field file. Available in the lammps/potentials directory.

control:

type: str

argument path: init_reaction_jdata/reaxff/control

Path to ReaxFF control file.

temp:

type: int | float

argument path: init_reaction_jdata/reaxff/temp

Target Temperature for the NVT MD simulation. Unit: K.

dt:

type: int | float

argument path: init_reaction_jdata/reaxff/dt

Real time for every time step. Unit: fs.

tau_t:

type: int | float

argument path: init_reaction_jdata/reaxff/tau_t

Time to determine how rapidly the temperature. Unit: fs.

dump_freq:

type: int

argument path: init_reaction_jdata/reaxff/dump_freq

Frequency of time steps to collect trajectory.

nstep:

type: int

argument path: init_reaction_jdata/reaxff/nstep

Total steps to run the ReaxFF MD simulation.

cutoff:

type: float

argument path: init_reaction_jdata/cutoff

Cutoff radius to take clusters from the trajectory. Note that only a complete molecule or free radical will be taken.

dataset_size:

type: int

argument path: init_reaction_jdata/dataset_size

Collected dataset size for each bond type.

qmkeywords:

type: str

argument path: init_reaction_jdata/qmkeywords

Gaussian keywords for first-principle calculations. e.g. force mn15/6-31g** Geom=PrintInputOrient. Note that “force” job is necessary to collect data. Geom=PrintInputOrient should be used when there are more than 50 atoms in a cluster.