init_reaction

init_reaction#

dpgen init_reaction is a workflow to initialize data for reactive systems of small gas-phase molecules. The workflow was introduced in the “Initialization” section of Energy & Fuels, 2021, 35 (1), 762–769.

To start the workflow, one needs a box containing reactive systems. The following packages are required for each of the step:

The Exploring step uses LAMMPS pair_style reaxff to run a short ReaxMD NVT MD simulation. In the Sampling step, molecular clusters are taken and k-means clustering algorithm is applied to remove the redundancy, which is described in Nature Communications, 11, 5713 (2020). The Labeling step calculates energies and forces using the Gaussian package.

An example of reaction.json is given below:

 1{
 2    "type_map": [
 3        "H",
 4        "O"
 5    ],
 6    "reaxff": {
 7        "data": "data.hydrogen",
 8        "ff": "ffield.reax.cho",
 9        "control": "lmp_control",
10        "temp": 3000,
11        "tau_t": 100,
12        "dt": 0.1,
13        "nstep": 10000,
14        "dump_freq": 100
15    },
16    "cutoff": 3.5,
17    "dataset_size": 100,
18    "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient"
19}

For detailed parameters, see parameters and machine parameters.

The generated data can be used to continue DP-GEN concurrent learning workflow. Read Energy & Fuels, 2021, 35 (1), 762–769 for details.