From dcac26513b988ed81625cdf7baf8a163d7c46877 Mon Sep 17 00:00:00 2001 From: Killian Date: Mon, 11 Mar 2024 18:19:27 -0400 Subject: [PATCH] bug fix --- examples/fcc_ternary_system.ipynb | 405 +++++++++++++++--------------- 1 file changed, 199 insertions(+), 206 deletions(-) diff --git a/examples/fcc_ternary_system.ipynb b/examples/fcc_ternary_system.ipynb index f7fe539..023d9e1 100644 --- a/examples/fcc_ternary_system.ipynb +++ b/examples/fcc_ternary_system.ipynb @@ -16,7 +16,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 22, "metadata": {}, "outputs": [], "source": [ @@ -45,7 +45,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 23, "metadata": {}, "outputs": [], "source": [ @@ -78,7 +78,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 24, "metadata": {}, "outputs": [ { @@ -158,7 +158,7 @@ "Ni + 4⋅Cr ⋅Ni + Cr⋅Ni + Ni " ] }, - "execution_count": 3, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } @@ -189,7 +189,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 25, "metadata": {}, "outputs": [ { @@ -225,7 +225,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 26, "metadata": {}, "outputs": [], "source": [ @@ -247,7 +247,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 27, "metadata": {}, "outputs": [ { @@ -267,193 +267,193 @@ "data": { "text/html": [ "
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\u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m2.0\u001b[0m, \u001b[1;36m5.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m372\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m3.0\u001b[0m, \u001b[1;36m4.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m606\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m4.0\u001b[0m, \u001b[1;36m3.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m606\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m5.0\u001b[0m, \u001b[1;36m2.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m372\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m6.0\u001b[0m, \u001b[1;36m1.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m126\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m5.0\u001b[0m, \u001b[1;36m7.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m24\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m6.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, 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\u001b[1m(\u001b[0m\u001b[1;36m9.0\u001b[0m, \u001b[1;36m2.0\u001b[0m, \u001b[1;36m1.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m18\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m9.0\u001b[0m, \u001b[1;36m3.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m9\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m10.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, \u001b[1;36m2.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m10.0\u001b[0m, \u001b[1;36m1.0\u001b[0m, \u001b[1;36m1.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m,\n", " \u001b[1m(\u001b[0m\u001b[1;36m10.0\u001b[0m, \u001b[1;36m2.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m,\n", - " \u001b[1m(\u001b[0m\u001b[1;36m11.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, \u001b[1;36m1.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m,\n", - " \u001b[1m(\u001b[0m\u001b[1;36m11.0\u001b[0m, \u001b[1;36m1.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m,\n", - " \u001b[1m(\u001b[0m\u001b[1;36m12.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m4\u001b[0m\n", + " \u001b[1m(\u001b[0m\u001b[1;36m11.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, \u001b[1;36m1.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m1\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m11.0\u001b[0m, \u001b[1;36m1.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m1\u001b[0m,\n", + " \u001b[1m(\u001b[0m\u001b[1;36m12.0\u001b[0m, \u001b[1;36m0.0\u001b[0m, \u001b[1;36m0.0\u001b[0m\u001b[1m)\u001b[0m: \u001b[1;36m1\u001b[0m\n", "\u001b[1m}\u001b[0m\n" ] }, @@ -483,7 +483,7 @@ " np.array(list(df.counts)),\n", ")\n", "unique_concentrations, counts = np.unique(\n", - " shell_concentrations, axis=0, return_inverse=True\n", + " shell_concentrations, axis=0, return_counts=True\n", ")\n", "\n", "pattern = {\n", @@ -492,7 +492,7 @@ "}\n", "print(\"The machine learning pattern inventory is given by:\")\n", "print(pattern)\n", - "print(f\"We have a total of {len(counts)} distinct 1CP.\")" + "print(f\"We have a total of {np.sum(counts)} distinct 1CP.\")" ] }, { @@ -504,7 +504,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 28, "metadata": {}, "outputs": [], "source": [ @@ -531,7 +531,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 29, "metadata": {}, "outputs": [ { @@ -579,25 +579,25 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 34, "metadata": {}, "outputs": [ { "data": { "text/html": [ - "
The dissimilarity between these two motifs is: [0.14620305].\n",
+       "
The dissimilarity between these two motifs is: 0.15.\n",
        "\n",
-       "Before weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of [0] \n",
-       "since their central atom atomic types are the same. Their chemical composition dissimilarity is of [1.]/12 because \n",
-       "only two atoms are swapped. And their structural dissimilarity is of [0.28217429].\n",
+       "Before weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of 0.00 \n",
+       "since their central atom atomic types are the same. Their chemical composition dissimilarity is of 1.00/12 because \n",
+       "only two atoms are swapped. And their structural dissimilarity is of 0.28.\n",
        "
\n" ], "text/plain": [ - "The dissimilarity between these two motifs is: \u001b[1m[\u001b[0m\u001b[1;36m0.14620305\u001b[0m\u001b[1m]\u001b[0m.\n", + "The dissimilarity between these two motifs is: \u001b[1;36m0.15\u001b[0m.\n", "\n", - "Before weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of \u001b[1m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1m]\u001b[0m \n", - "since their central atom atomic types are the same. Their chemical composition dissimilarity is of \u001b[1m[\u001b[0m\u001b[1;36m1\u001b[0m.\u001b[1m]\u001b[0m\u001b[35m/\u001b[0m\u001b[95m12\u001b[0m because \n", - "only two atoms are swapped. And their structural dissimilarity is of \u001b[1m[\u001b[0m\u001b[1;36m0.28217429\u001b[0m\u001b[1m]\u001b[0m.\n" + "Before weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of \u001b[1;36m0.00\u001b[0m \n", + "since their central atom atomic types are the same. Their chemical composition dissimilarity is of \u001b[1;36m1.00\u001b[0m/\u001b[1;36m12\u001b[0m because \n", + "only two atoms are swapped. And their structural dissimilarity is of \u001b[1;36m0.28\u001b[0m.\n" ] }, "metadata": {}, @@ -625,15 +625,8 @@ ")\n", "\n", "\n", - "print(f\"The dissimilarity between these two motifs is: {d_ij}.\\n\\nBefore weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of {central_atom_dissim} since their central atom atomic types are the same. Their chemical composition dissimilarity is of {concentration_dissim}/12 because only two atoms are swapped. And their structural dissimilarity is of {structural_dissim}.\")" + "print(f\"The dissimilarity between these two motifs is: {d_ij[0]:.2f}.\\n\\nBefore weighthing based on the number of bonds of each structure, they have a central atom dissimilarity of {central_atom_dissim[0]:.2f} since their central atom atomic types are the same. Their chemical composition dissimilarity is of {concentration_dissim[0]:.2f}/12 because only two atoms are swapped. And their structural dissimilarity is of {structural_dissim[0]:.2f}.\")" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {