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update jupyter notebook
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@curtischong
curtischong committed Apr 18, 2024
1 parent ba0789f commit 85fa933
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313 changes: 246 additions & 67 deletions exploration/view_generated_results.ipynb
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"/Users/curtischong/Documents/dev/arreau/venv/lib/python3.11/site-packages/pymatgen/analysis/local_env.py:4148: UserWarning:\n",
"\n",
"No oxidation states specified on sites! For better results, set the site oxidation states in the structure.\n",
"\n",
"/Users/curtischong/Documents/dev/arreau/venv/lib/python3.11/site-packages/pymatgen/analysis/local_env.py:3941: UserWarning:\n",
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"CrystalNN: cannot locate an appropriate radius, covalent or atomic radii will be used, this can lead to non-optimal results.\n",
"\n"
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"\n",
"for i in range(20):\n",
" lattice, frac_x, atomic_numbers = get_one_crystal(sample_result, i)\n",
" print(lattice)\n",
" #frac_x -= np.min(frac_x, axis=0)\n",
" #tiled_lattice, tiled_species, tiled_coordinates = tile_structure(lattice, atomic_numbers, frac_x, 2)\n",
" #display(Structure(tiled_lattice, tiled_species, tiled_coordinates))\n",
" #print(lattice)\n",
" frac_x -= np.min(frac_x, axis=0)\n",
" tiled_lattice, tiled_species, tiled_coordinates = tile_structure(lattice, atomic_numbers, frac_x, 2)\n",
" display(Structure(tiled_lattice, tiled_species, tiled_coordinates))\n",
"\n",
"#fig = plot_crystal(atomic_numbers, lattice, frac_x, show_bonds=False)\n",
"#display(fig)"
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20 changes: 10 additions & 10 deletions main_diffusion_generate.py
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Expand Up @@ -97,19 +97,19 @@ def generate_n_crystals(
if __name__ == "__main__":
num_atoms = 4
# use_constant_atomic_symbols = ["Ac", "Ac", "Ir", "Ag"]
use_constant_atomic_symbols = ["C", "C", "C", "C", "C", "C", "C", "C"]
# use_constant_atomic_symbols = None
# use_constant_atomic_symbols = ["C", "C", "C", "C", "C", "C", "C", "C"]
use_constant_atomic_symbols = None

if use_constant_atomic_symbols is not None:
num_atoms = len(use_constant_atomic_symbols)

generate_single_crystal(
num_atoms=num_atoms,
visualization_setting=VisualizationSetting.ALL_DETAILED,
use_constant_atomic_symbols=use_constant_atomic_symbols,
)
# generate_n_crystals(
# num_crystals=20,
# num_atoms_per_sample=4,
# generate_single_crystal(
# num_atoms=num_atoms,
# visualization_setting=VisualizationSetting.ALL,
# use_constant_atomic_symbols=use_constant_atomic_symbols,
# )
generate_n_crystals(
num_crystals=20,
num_atoms_per_sample=8,
use_constant_atomic_symbols=use_constant_atomic_symbols,
)

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