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Notebook 01 mse2023 feeback #5

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Notebook 01 mse2023 feeback #5

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17 changes: 12 additions & 5 deletions 01-Atomic_scale_structures.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -408,7 +408,8 @@
" assert isinstance(output, ase.Atoms), f\"TypeAssert failed: Expected type ase.Atoms but got {type(output)}.\"\n",
" assert len(output) == 1, f\"LenAssert failed: Expected length 1 but got {len(output)}.\"\n",
" assert np.sum(84 == output.numbers) == 1, f\"One Polonium is expected in the molecule. Found {np.sum(84 == output.numbers)} Polonium atom(s).\"\n",
" assert np.allclose(output.cell,3.3596173*np.eye(3)), f\"Unit cell has wrong dimensions.\"\n",
" assert output.cell.shape == (3,3), f\"Unit cell has wrong dimensions.\"\n",
" assert np.allclose(output.cell, 3.3596173*np.eye(3), atol=1e-5,) f\"Unit cell is not correct or not accurate enough.\"\n",
" return fingerprint_ase_atoms(output)\n",
" \n",
" \n",
Expand Down Expand Up @@ -439,10 +440,16 @@
"source": [
"Periodic boundary conditions are not only used to model perfect crystals. They are also used as a practical way to describe bulk systems, while using a finite number of atomic degrees of freedom: the size of the cell and the coordinates of the atoms in a single repeate unit. Compare these two systems:\n",
"\n",
"a) a finite-sized droplet with 10 water molecules\n",
"<img src=\"figures/pbc-1.png\" width=\"400\"/>\n",
"b) a periodic system with a repeat unit of 10 water molecules\n",
"<img src=\"figures/pbc-2.png\" width=\"400\"/>"
"<table style=\"width:100%\">\n",
" <tr>\n",
" <th>a) a finite-sized droplet with 10 water molecules</th>\n",
" <th>b) a periodic system with a repeat unit of 10 water molecules</th>\n",
" </tr>\n",
" <tr>\n",
" <th><img src=\"figures/pbc-1.png\" width=\"400\"/></th>\n",
" <th><img src=\"figures/pbc-2.png\" width=\"400\"/></th>\n",
" </tr>\n",
"</table>"
]
},
{
Expand Down