Some basic interactions with scf.py

b780462b · moritz.buchhorn · 1791295c · b780462b
Commit b780462b authored 5 months ago by moritz.buchhorn
--- a/02-scf/02-scf.ipynb
+++ b/02-scf/02-scf.ipynb
@@ -14,12 +14,106 @@
   "execution_count": null,
   "metadata": {},
   "outputs": [],
-   "source": []
+   "source": [
+    "import scf\n",
+    "import numpy as np\n",
+    "from pyscf import gto\n",
+    "import plotly.graph_objects as go"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "coordinates='''\n",
+    "    C  0.00  0.00  0.00\n",
+    "    O  0.00  1.54  0.00\n",
+    "    O  0.00 -1.54  0.00\n",
+    "'''\n",
+    "\n",
+    "# To build such a molecule object, specific information is required, which is defined in the following code line. (In this oversimplified case, only the molecular coordinates and the basis set are used.) With this information, PySCF can now calculate the individual system-dependent parameters.\n",
+    "\n",
+    "\n",
+    "mol = gto.M(atom=coordinates, basis='sto-3g')\n",
+    "\n",
+    "# nuclei-nuclei potential\n",
+    "E_nuc  = mol.energy_nuc()\n",
+    "\n",
+    "# number of atomic orbitals\n",
+    "NAO = mol.nao\n",
+    "# number of electrons\n",
+    "NEL = mol.nelectron\n",
+    "\n",
+    "# overlap integrals\n",
+    "S= mol.intor('int1e_ovlp')\n",
+    "# kinetic energy integrals\n",
+    "T_e = mol.intor('int1e_kin')\n",
+    "# electrons-nuclei potential energy integrals\n",
+    "V_ne = mol.intor('int1e_nuc')\n",
+    "\n",
+    "# two electron Coulomb integrals\n",
+    "J = mol.intor('int2e')\n",
+    "\n",
+    "\n",
+    "Hc = scf.build_hc(T_e, V_ne)\n",
+    "X = scf.build_ortho_mat(S)\n",
+    "finished_scf = scf.scf(Hc,X,J, E_nuc, NAO, NEL)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig = go.Figure()\n",
+    "\n",
+    "fig.add_trace(go.Scatter(\n",
+    "    x = list(range(finished_scf[\"iterations\"])),\n",
+    "    y = finished_scf[\"tot_energies\"],\n",
+    "))\n",
+    "\n",
+    "fig.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig = go.Figure()\n",
+    "\n",
+    "orb_eigenvalues = finished_scf[\"orb_eigenvalues\"].T\n",
+    "for i in range(len(orb_eigenvalues)):\n",
+    "    fig.add_trace(go.Scatter(\n",
+    "        x = list(range(finished_scf[\"iterations\"])),\n",
+    "        y = orb_eigenvalues[i],\n",
+    "    ))\n",
+    "\n",
+    "fig.show()"
+   ]
  }
 ],
 "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
  "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.10"
  }
 },
 "nbformat": 4,

 %% Cell type:markdown id: tags:

 # B.CTC: SCF

 In diesem Notebook werden wir einen auf das Nötigste reduzierten SCF-Code verwenden, um einen Einblick in die einzelnen Iterationen zu gewinnen.

 %% Cell type:code id: tags:

-``` 
+``` python
+import scf
+import numpy as np
+from pyscf import gto
+import plotly.graph_objects as go
+```
+
+%% Cell type:code id: tags:
+
+``` python
+coordinates='''
+    C  0.00  0.00  0.00
+    O  0.00  1.54  0.00
+    O  0.00 -1.54  0.00
+'''
+
+# To build such a molecule object, specific information is required, which is defined in the following code line. (In this oversimplified case, only the molecular coordinates and the basis set are used.) With this information, PySCF can now calculate the individual system-dependent parameters.
+
+
+mol = gto.M(atom=coordinates, basis='sto-3g')
+
+# nuclei-nuclei potential
+E_nuc  = mol.energy_nuc()
+
+# number of atomic orbitals
+NAO = mol.nao
+# number of electrons
+NEL = mol.nelectron
+
+# overlap integrals
+S= mol.intor('int1e_ovlp')
+# kinetic energy integrals
+T_e = mol.intor('int1e_kin')
+# electrons-nuclei potential energy integrals
+V_ne = mol.intor('int1e_nuc')
+
+# two electron Coulomb integrals
+J = mol.intor('int2e')
+
+
+Hc = scf.build_hc(T_e, V_ne)
+X = scf.build_ortho_mat(S)
+finished_scf = scf.scf(Hc,X,J, E_nuc, NAO, NEL)
+```
+
+%% Cell type:code id: tags:
+
+``` python
+fig = go.Figure()
+
+fig.add_trace(go.Scatter(
+    x = list(range(finished_scf["iterations"])),
+    y = finished_scf["tot_energies"],
+))
+
+fig.show()
+```
+
+%% Cell type:code id: tags:
+
+``` python
+fig = go.Figure()
+
+orb_eigenvalues = finished_scf["orb_eigenvalues"].T
+for i in range(len(orb_eigenvalues)):
+    fig.add_trace(go.Scatter(
+        x = list(range(finished_scf["iterations"])),
+        y = orb_eigenvalues[i],
+    ))
+
+fig.show()
 ```