update notebooks

example/notebook/e-ph.ipynb

@@ -12,6 +12,7 @@
    "metadata": {},
    "source": [
     "First, we calculate the overlap `<ψ_i(0)|ψ_f(Q)>` and its derivative.  \n",
+    "`ψ_i(0)` is a perturbed band-edge state, and `ψ_f(Q)` is a localized defect state at the configuration coordinate `Q` which can be calculated using `get_del_Q.py`.\n",
     "The electron-phonon coupling matrix element is given by   \n",
     "`W_if = (ε_f - ε_i) d <ψ_i(0)|ψ_f(Q)> / dQ`.\n",
     "\n",
@@ -36,7 +37,7 @@
    "metadata": {},
    "source": [
     "```bash\n",
-    "$ python get_wf.py   -d 288 -b 291  -D DISP_000 -i DISP_-02 DISP_-01 DISP_001 DISP_002\n",
+    "$ python get_wf.py   -d <band_index of ψ_i> -b <band_index of ψ_f>  -D <path to the initial geometry> -i <path to the deformed geometry 1> [<path to the deformed geometry 2> ...]\n",
     "\n",
     "GRID ENCUT 918.2911873931497\n",
     "finished making projector list\n",
@@ -68,14 +69,14 @@
    "source": [
     "## W_if calculation\n",
     "\n",
-    "Use `get_del_Q.py` to get a distance between structures (`ΔQ`).\n",
+    "Use `get_del_Q.py` to get a distance between structures (`ΔQ`) in `amu^0.5Å`. `ΔQ` is a collective variable of the mass-weighted deformation `ΔQ = ΣmΔ𝐑`.\n",
     "\n",
-    "`ϵ_i` and `ϵ_f` are KS eigenvalues of the initla and final states.\n"
+    "`ϵ_i` and `ϵ_f` are KS eigenvalues of the initial (`ψ_i(0)`) and final states (`ψ_f(Q_f)`).\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -89,7 +90,7 @@
    "source": [
     "# using Plots\n",
     "# \n",
-    "ΔQ = 0.18059526482789678 # ΔQ between DISP_000 and DISP_001\n",
+    "ΔQ = 0.18059526482789678 # ΔQ between DISP_000 and DISP_001 in [amu^0.5Å]\n",
     "ϵ_f = 5.405963  # unoccupied trap\n",
     "ϵ_i = 6.227692  # CBM\n",
     "\n",
@@ -104,13 +105,6 @@
     "println(\"W_if_n = \", W_if_n)\n",
     "# plot(overlap)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {