convert to mkdoc

.gitignore

 *~
 .ipynb_checkpoints
-_book
-node_modules
+site
+

SUMMARY.md

-# Summary
-
-* [Phonons and specific Heat](lecture_1.md)
-* [Free electron model](lecture_2.md)
-* [Atoms and bonds](lecture_3.md)
-* [Electrons and phonons in 1D](lecture_4.md)
-* [Crystal structure and diffraction](lecture_5.md)
-* [Tight binding and nearly free electrons](lecture_6.md)
-* [Semiconductors](lecture_7.md)
-* Magnetism

code/band_structures.py

@@ -140,7 +140,7 @@ def DOS_finite_electron_chain(n, output_name):
 
 
 def main():
-    os.chdir('figures')
+    os.chdir('doc/figures')
     fermi_dirac()
     phonons_1d()
     phonons_1d_2masses()

code/bands_2d.py

@@ -76,7 +76,7 @@ def plot_nfem():
             )
         )
     )
-    with open('figures/nfem_2d.html', 'w') as f:
+    with open('doc/figures/nfem_2d.html', 'w') as f:
         f.write(figure_html(figure=
             py.plot(fig, show_link=False, 
                     output_type='div', include_plotlyjs=False)
@@ -112,7 +112,7 @@ def plot_tb():
             )
         )
     )
-    with open('figures/tb_2d.html', 'w') as f:
+    with open('doc/figures/tb_2d.html', 'w') as f:
         f.write(figure_html(figure=
             py.plot(fig, show_link=False, 
                     output_type='div', include_plotlyjs=False)