From 58f899ddbe8de01ca008ca78c2c977381d23989b Mon Sep 17 00:00:00 2001
From: Dou Du <dou.du@icloud.com>
Date: Sat, 27 Apr 2024 15:47:56 +0200
Subject: [PATCH] fix the pseudopotential bugs

---
 notebook/band-theory/pseudopotential.ipynb | 67 +++++++++++++---------
 1 file changed, 39 insertions(+), 28 deletions(-)

diff --git a/notebook/band-theory/pseudopotential.ipynb b/notebook/band-theory/pseudopotential.ipynb
index 36c4611..a0fdb13 100644
--- a/notebook/band-theory/pseudopotential.ipynb
+++ b/notebook/band-theory/pseudopotential.ipynb
@@ -277,7 +277,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "img = plt.figure(tight_layout=True, figsize=(9,9))\n",
@@ -395,13 +397,13 @@
     "    x1 = np.arange(0, 50.0, 0.01)\n",
     "    y1 = rf(x1)*x1\n",
     "    line_rho.set_data([x1, y1])\n",
-    "    line_rc1.set_data(s_rc.value, [-1, 1])\n",
+    "    line_rc1.set_data([s_rc.value], [-1, 1])\n",
     "    ann_rc.set_position((s_rc.value + 1.0, rf(s_rc.value)*s_rc.value))\n",
     "\n",
     "    x2 = np.arange(0, 50.0, 0.01)\n",
     "    y2 = (rf(x2)*x2)**2\n",
     "    line_rho2.set_data([x2, y2])\n",
-    "    line_rc2.set_data(s_rc.value, [-1, 1])\n",
+    "    line_rc2.set_data([s_rc.value], [-1, 1])\n",
     "    ann_rc2.set_position((s_rc.value + 1.0, (rf(s_rc.value)*s_rc.value)**2))\n",
     "  \n",
     "\n",
@@ -420,17 +422,19 @@
     "    line_logdr_ps.set_data([],[])\n",
     "    \n",
     "    # line_logdr_rho.set_data([x3, y3])\n",
-    "    line_rc3.set_data(s_rc.value, [-1, 1])\n",
-    "    line_rc4.set_data(s_rc.value, [-1, 1])\n",
+    "    line_rc3.set_data([s_rc.value], [-1, 1])\n",
+    "    line_rc4.set_data([s_rc.value], [-1, 1])\n",
     "\n",
     "    ann_rc2.set_position((s_rc.value + 1.0, (rf(s_rc.value)*s_rc.value)**2))\n",
     "  \n",
-    "    \n",
-    "\n",
-    "    ax1.collections.clear()\n",
-    "    ax2.collections.clear()\n",
-    "    ax3.collections.clear()\n",
+    "    for line in ax1.collections:\n",
+    "        line.remove()\n",
+    "        \n",
+    "    for line in ax2.collections:\n",
+    "        line.remove()\n",
     "\n",
+    "    for line in ax3.collections:\n",
+    "        line.remove()\n",
     "\n",
     "    ax2.fill_between(x2, y2, 0, where=x2<s_rc.value, facecolor='yellow', alpha=0.5)\n",
     "    ax1.hlines(0, 0, 50, 'k','--')\n",
@@ -440,8 +444,8 @@
     "    line_pswf2.set_data([],[])\n",
     "\n",
     "    line_psv.set_data([],[])\n",
-    "    point.set_data(s_rc.value, rf(s_rc.value)*s_rc.value)\n",
-    "    point2.set_data(s_rc.value, (rf(s_rc.value)*s_rc.value)**2)\n",
+    "    point.set_data([s_rc.value], [rf(s_rc.value)*s_rc.value])\n",
+    "    point2.set_data([s_rc.value], [(rf(s_rc.value)*s_rc.value)**2])\n",
     "\n",
     "    ax1.set_ylim([y1.min()-0.04, y1.max()+0.04])\n",
     "    ax2.set_ylim([y2.min()-0.04, y2.max()+0.04])\n",
@@ -466,15 +470,21 @@
     "    x2 = np.arange(0, 50.0, 0.01)\n",
     "    y2 = (rf(x2)*x2)**2\n",
     "    \n",
-    "    line_rc1.set_data(s_rc.value, [-1, 1])\n",
-    "    line_rc2.set_data(s_rc.value, [-1, 1])\n",
-    "    line_rc3.set_data(s_rc.value, [-1, 1])\n",
-    "    line_rc4.set_data(s_rc.value, [-1, 1])\n",
+    "    line_rc1.set_data([s_rc.value], [-1, 1])\n",
+    "    line_rc2.set_data([s_rc.value], [-1, 1])\n",
+    "    line_rc3.set_data([s_rc.value], [-1, 1])\n",
+    "    line_rc4.set_data([s_rc.value], [-1, 1])\n",
     "\n",
     "    ann_rc.set_position((s_rc.value + 1.0, rf(s_rc.value)*s_rc.value))\n",
-    "    ax1.collections.clear()\n",
-    "    ax2.collections.clear()\n",
-    "    ax3.collections.clear()\n",
+    "    \n",
+    "    for line in ax1.collections:\n",
+    "        line.remove()\n",
+    "        \n",
+    "    for line in ax2.collections:\n",
+    "        line.remove()\n",
+    "\n",
+    "    for line in ax3.collections:\n",
+    "        line.remove()\n",
     "\n",
     "\n",
     "    ax2.fill_between(x2, y2, 0, where=x2<s_rc.value, facecolor='yellow', alpha=0.5)\n",
@@ -482,8 +492,9 @@
     "    line_pswf.set_data([],[])\n",
     "    line_pswf2.set_data([],[])\n",
     "    line_psv.set_data([],[])\n",
-    "    point.set_data(s_rc.value, rf(s_rc.value)*s_rc.value)\n",
-    "    point2.set_data(s_rc.value, (rf(s_rc.value)*s_rc.value)**2)\n",
+    "    point.set_data([s_rc.value], rf(s_rc.value)*s_rc.value)\n",
+    "    point2.set_data([s_rc.value], (rf(s_rc.value)*s_rc.value)**2)\n",
+    "    ax1.hlines(0, 0, 50, 'k','--')\n",
     "\n",
     "    clear_texts()\n",
     "     \n",
@@ -583,8 +594,8 @@
     "    # x3 = np.linspace(0, rc, 800);\n",
     "    x3 = np.arange(0, 50.0, 0.01)\n",
     "\n",
-    "    line_pswf.set_data(x1, psf(x1));\n",
-    "    line_pswf2.set_data(x2, psf2(x2));\n",
+    "    line_pswf.set_data([x1], [psf(x1)]);\n",
+    "    line_pswf2.set_data([x2], [psf2(x2)]);\n",
     "\n",
     "    ax2.fill_between(x2, psf2(x2), 0, where=x2<s_rc.value, facecolor='green', alpha=0.5)\n",
     "    \n",
@@ -595,10 +606,10 @@
     "    logr = diff(ho, r).subs(r, rc).evalf()/ho.subs(r, rc).evalf()\n",
     "    \n",
     "        \n",
-    "    line_logdr_rho.set_data(x3,logr_r(x3))\n",
-    "    line_logdr_ps.set_data(x3,logl_r(x3))\n",
+    "    line_logdr_rho.set_data([x3],[logr_r(x3)])\n",
+    "    line_logdr_ps.set_data([x3],[logl_r(x3)])\n",
     "    \n",
-    "    point3.set_data(s_rc.value, logr_r(s_rc.value))\n",
+    "    point3.set_data([s_rc.value], [logr_r(s_rc.value)])\n",
     "    ann_rc3.remove()\n",
     "    ann_rc3 = ax3.annotate(\"$R_c$\", xy=(s_rc.value + 1.0,logr_r(s_rc.value)) , fontsize=20)\n",
     "    # ann_rc3.set_position((s_rc.value + 1.0,logr_r(s_rc.value)))\n",
@@ -640,7 +651,7 @@
     "        \n",
     "    x1 = np.linspace(0.001, rc, 800);\n",
     "    x2 = np.linspace(rc, 50, 800);\n",
-    "    line_psv.set_data(np.concatenate((x1,x2)), np.concatenate((psfnl(x1),psfnr(x2))));\n",
+    "    line_psv.set_data([np.concatenate((x1,x2))], [np.concatenate((psfnl(x1),psfnr(x2)))]);\n",
     "    ax4.set_ylim([psfnl(x1).min(axis=0)-0.05, max(psfnl(x1).max(axis=0)+0.1, 0.05)])\n",
     "\n",
     "def compute_pseudopotential(c):\n",
@@ -733,7 +744,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.11.7"
   },
   "voila": {
    "authors": "Dou Du and Giovanni Pizzi"