Env setup

[huangchieh]

cd /scratch/phys/project/sin/hackathon 
srun -p gpu-debug --gres=gpu:1   --time=00:30:00 --mem=16G --pty bash
module load mamba gcc cuda
conda activate /scratch/phys/project/sin/hackathon/.conda_envs/hack
python train.py --config configs/synth_3D.yaml --cuda_visible_device 0 --nproc_per_node 1

[huangchieh]

Dataset

/scratch/phys/project/sin/AFM_Hartree_DB/AFM_sims/striped/SIN-AFM

[huangchieh]

How to define the size of the bounding box?
We can define a cubic with a size of (vdw_radii + offset), where offset can be a number >= 0.

from ase.data import vdw_radii
print(vdw_radii[1])  # Get the radius for Hydrogen (atomic number 1)