Small changes

b74277c0 · moritz.buchhorn · b780462b · b74277c0 · b74277c0
Commit b74277c0 authored 5 months ago by moritz.buchhorn
--- a/02-scf/02-scf.ipynb
+++ b/02-scf/02-scf.ipynb
@@ -27,15 +27,14 @@
   "metadata": {},
   "outputs": [],
   "source": [
+    "# 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",
    "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",
@@ -47,7 +46,7 @@
    "NEL = mol.nelectron\n",
    "\n",
    "# overlap integrals\n",
-    "S= mol.intor('int1e_ovlp')\n",
+    "S = mol.intor('int1e_ovlp')\n",
    "# kinetic energy integrals\n",
    "T_e = mol.intor('int1e_kin')\n",
    "# electrons-nuclei potential energy integrals\n",
@@ -95,6 +94,17 @@
    "\n",
    "fig.show()"
   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "np.set_printoptions(suppress=True, precision=2)\n",
+    "[print((\"{:6.2f}\"*len(line)).format(*line)) for line in finished_scf[\"coefficients\"][-1].T]\n",
+    "# finished_scf[\"coefficients\"][70].T"
+   ]
  }
 ],
 "metadata": {
@@ -113,7 +123,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.13"
  }
 },
 "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
+# 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.
+
 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')
+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()
 ```
+
+%% Cell type:code id: tags:
+
+``` python
+np.set_printoptions(suppress=True, precision=2)
+[print(("{:6.2f}"*len(line)).format(*line)) for line in finished_scf["coefficients"][-1].T]
+# finished_scf["coefficients"][70].T
+```

--- a/02-scf/scf.py
+++ b/02-scf/scf.py
 #!/usr/bin/env python
 # coding: utf-8

-from pyscf import gto
 import numpy as np


@@ -89,6 +88,8 @@ def scf(Hc: np.array, X: np.array, J: np.array, E_nuc: float, NAO: int, NEL: int
    this_scf = {
        "tot_energies": [E_tot_0],
        "orb_eigenvalues": [e_0],
+        "coefficients": [C_0],
+        "iterations": 0
    }

    # SCF loop
@@ -101,13 +102,14 @@ def scf(Hc: np.array, X: np.array, J: np.array, E_nuc: float, NAO: int, NEL: int
        e, C = solve_eigenvalue(Fp, X)
        
        P = build_density(C, NAO, NEL)
-    
+        
        E_el = electronic_energy(P, Hc, F, NAO)
        
        E_tot = E_el + E_nuc

        this_scf["tot_energies"].append(E_tot)
        this_scf["orb_eigenvalues"].append(e)
+        this_scf["coefficients"].append(C)
            
        if np.abs(E_el-E_el_0)<delta_E:
            print("E_el converged after: "+str(i)+" Iterations.")