diff --git a/Lesson4_DeepPot.ipynb b/Lesson4_DeepPot.ipynb index a38b0ea..8f366fd 100644 --- a/Lesson4_DeepPot.ipynb +++ b/Lesson4_DeepPot.ipynb @@ -78,7 +78,7 @@ "metadata": { "id": "jvwwiTzS_yxR" }, - "execution_count": 1, + "execution_count": null, "outputs": [] }, { @@ -155,7 +155,7 @@ "metadata": { "id": "v9RdVoWhpVBi" }, - "execution_count": 2, + "execution_count": null, "outputs": [] }, { @@ -188,12 +188,12 @@ "s(R_{1i}) & s(R_{1i}) \\frac{x_{1i}}{R_{1i}} & s(R_{1i}) \\frac{y_{1i}}{R_{1i}} & s(R_{1i}) \\frac{z_{1i}}{R_{1i}} \\\\ \\\\\n", "s(R_{2i}) & s(R_{2i}) \\frac{x_{2i}}{R_{2i}} & s(R_{2i}) \\frac{y_{i1}}{R_{2i}} & s(R_{2i}) \\frac{z_{2i}}{R_{2i}} \\\\ \\\\\n", "\\cdots & \\cdots & \\cdots & \\cdots \\\\ \\\\\n", - "s(R_{ni}) & s(R_{ni}) \\frac{x_{ni}}{R_{ni}} & s(R_{ni}) \\frac{y_{ni}}{R_{ni}} & s(R_{ni}) \\frac{z_{ni}}{R_{ni}}\n", + "s(R_{n_ii}) & s(R_{n_ii}) \\frac{x_{n_ii}}{R_{n_ii}} & s(R_{n_ii}) \\frac{y_{n_ii}}{R_{n_ii}} & s(R_{n_ii}) \\frac{z_{n_ii}}{R_{n_ii}}\n", "\\end{pmatrix}\n", "\\end{eqnarray}$$\n", "
\n", "\n", - "where $n$ is the number of neighbors for the atom. $s$ is the weighting function.\n", + "where $n_i$ is the number of neighbors for atom $i$ and $s$ is the weighting function.\n", "\n", "$$\\begin{eqnarray}\n", "s(R_{ji}) =\n", @@ -233,7 +233,7 @@ "metadata": { "id": "6CksVhkaqA9e" }, - "execution_count": 3, + "execution_count": null, "outputs": [] }, { @@ -262,7 +262,7 @@ "Now we use embedding neural networks to transform each of the $s$ values into $M_1$ numbers. This gives us the local embedding matrix $\\mathcal{G}$. Note the embedding neural network parameters depend on the chemical species of atom $i$ and atom $j$. \n", "\n", "$$\\begin{eqnarray}\n", - "{\\mathcal{G}}_i\n", + "g_i\n", "= \\begin{pmatrix}\n", "\\left( G[s(R_{1i})] \\right)_1 &\n", "\\left( G[s(R_{1i})] \\right)_2 & \\cdots &\n", @@ -270,17 +270,17 @@ "\\left( G[s(R_{2i})] \\right)_1 &\n", "\\left( G[s(R_{2i})] \\right)_2 & \\cdots & \\left( G[s(R_{2i})] \\right)_{m_1} \\\\\n", "\\cdots & \\cdots & \\cdots & \\cdots \\\\\n", - "\\left( G[s(R_{ni})] \\right)_1 &\n", - "\\left( G[s(R_{ni})] \\right)_2 & \\cdots & \\left( G [s(R_{ni})] \\right)_{m_1}\n", + "\\left( G[s(R_{n_ii})] \\right)_1 &\n", + "\\left( G[s(R_{n_ii})] \\right)_2 & \\cdots & \\left( G [s(R_{n_ii})] \\right)_{m_1}\n", "\\end{pmatrix}\n", "\\end{eqnarray}$$\n", "\n", - "Two local embedding matrices are used: $\\mathcal{G}_{i1}$ is $n\\times M_1$ dimensions, while $\\mathcal{G}_{i2}$ is $n\\times M_2$ dimensions. The dimensions $M_1$ and $M_2$ represent the number of neural network parameters, where $M_1$ is larger than $M_2$.\n", + "Two local embedding matrices are used: $g_{i}^{1}$ is $n\\times M_1$ dimensions, while $g_{i}^{2}$ is $n\\times M_2$ dimensions. The dimensions $M_1$ and $M_2$ represent the number of neural network parameters, where $M_1$ is larger than $M_2$.\n", "\n", - "By multiplying our local embedding matrices and environment matrices, we can preserve the translational, rotational, and permutational symmetry in the form of the encoded feature matrix $\\mathcal{D_i}$ \n", + "By multiplying our local embedding matrices and environment matrices, we can preserve the translational, rotational, and permutational symmetry in the form of the encoded feature matrix $D_i$ \n", "\n", "$$\\begin{eqnarray}\n", - "{\\mathcal{D}}_i = \\left( {\\mathcal{G}}_i^1 \\right)^T {\\mathcal{R}}_i {\\mathcal{R}}_i^T {\\mathcal{G}}_i^2\n", + "D_i = \\left( g_i^1 \\right)^T {\\mathcal{R}}_i {\\mathcal{R}}_i^T g_i^2\n", "\\end{eqnarray}$$\n", "\n", "The local feature matrix is then mapped to the atomic energy using the fitting neural network. Finally, the atomic energies are summed to yield the total energy of the molecule." @@ -303,7 +303,7 @@ "source": [ "### The Feature Class\n", "\n", - "Here we define the feature class, which uses the local environment matrix ($\\mathcal{R}_i$) and local embedding matrices ($\\mathcal{G}^1_i$ and $\\mathcal{G}^2_i$) to construct the encoded feature matrix ($\\mathcal{D}_i$)." + "Here we define the feature class, which uses the local environment matrix ($\\mathcal{R}_i$) and local embedding matrices ($g^1_i$ and $g^2_i$) to construct the encoded feature matrix ($D_i$)." ], "metadata": { "id": "w7XZmhe7d1gW" @@ -348,7 +348,7 @@ "metadata": { "id": "WY8A0MmNqnvM" }, - "execution_count": 4, + "execution_count": null, "outputs": [] }, { @@ -381,7 +381,7 @@ "metadata": { "id": "KWF2_lClqvpN" }, - "execution_count": 5, + "execution_count": null, "outputs": [] }, { @@ -431,7 +431,7 @@ "metadata": { "id": "kfEi4Ffrq196" }, - "execution_count": 6, + "execution_count": null, "outputs": [] }, { @@ -489,7 +489,7 @@ }, "outputId": "82951cc4-9756-46bc-dc5e-a6443b3462df" }, - "execution_count": 7, + "execution_count": null, "outputs": [ { "output_type": "stream", @@ -562,7 +562,7 @@ }, "outputId": "5be04806-9a15-46ab-99e0-cc92f5effe23" }, - "execution_count": 8, + "execution_count": null, "outputs": [ { "output_type": "display_data", @@ -606,7 +606,7 @@ }, "outputId": "61f07938-3b0e-4b03-9197-3fdf5d9896c5" }, - "execution_count": 9, + "execution_count": null, "outputs": [ { "output_type": "display_data",