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fix the pseudopotential bugs #323

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May 4, 2024
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fix the pseudopotential bugs #323

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67 changes: 39 additions & 28 deletions notebook/band-theory/pseudopotential.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -466,24 +470,31 @@
" 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",
" ax2.hlines(0, 0, 50, 'k','--')\n",
" 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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
Expand Down
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