chore: rename bands and dos calculation files according to convention

docs/hands-on/bands.mdx

@@ -8,14 +8,14 @@ consistent field calculation](scf). We have our input `scf` file with some new
 parameters:
 
 import CodeBlock from '@theme/CodeBlock';
-import si_bands_scf_in from '!!raw-loader!/src/silicon/si_bands_scf.in';
+import si_bands_scf_in from '!!raw-loader!/src/silicon/pw.scf.silicon_bands.in';
 
-<CodeBlock language="bash" title="src/silicon/si_bands_scf.in" showLineNumbers>{si_bands_scf_in}</CodeBlock>
+<CodeBlock language="bash" title="src/silicon/pw.scf.silicon_bands.in" showLineNumbers>{si_bands_scf_in}</CodeBlock>
 
 Run the `scf` calculation:
 
 ```bash
-pw.x < si_bands_scf.in > si_bands_scf.out
+pw.x < pw.scf.silicon_bands.in > pw.scf.silicon_bands.out
 ```
 
 Next step is our band calculation (non-self consistent field) calculation. The
@@ -33,28 +33,28 @@ also in the unoccupied bands above the Fermi energy. Number of occupied bands
 can be found in the `scf` output as number of Kohn-Sham states. Below is a
 sample input file for the band calculation:
 
-import si_bands_in from '!!raw-loader!/src/silicon/si_bands.in';
+import si_bands_in from '!!raw-loader!/src/silicon/pw.bands.silicon.in';
 
-<CodeBlock language="bash" title="src/silicon/si_bands.in" showLineNumbers>{si_bands_in}</CodeBlock>
+<CodeBlock language="bash" title="src/silicon/pw.bands.silicon.in" showLineNumbers>{si_bands_in}</CodeBlock>
 
 Run `pw.x` with `bands` calculation input file:
 
 ```bash
-pw.x < si_bands.in > si_bands.out
+pw.x < pw.bands.silicon.in > pw.bands.silicon.out
 ```
 
 After the bands calculation is performed, we need some postprocessing using
 `bands.x` utility in order to obtain the data in more usable format. Input file
 for `bands.x` postprocessing:
 
-import si_bands_pp_in from '!!raw-loader!/src/silicon/si_bands_pp.in';
+import si_bands_pp_in from '!!raw-loader!/src/silicon/pp.bands.silicon.in';
 
-<CodeBlock language="bash" title="src/silicon/si_bands_pp.in" showLineNumbers>{si_bands_pp_in}</CodeBlock>
+<CodeBlock language="bash" title="src/silicon/pp.bands.silicon.in" showLineNumbers>{si_bands_pp_in}</CodeBlock>
 
 Run `bands.x` from post processing (PP) module:
 
 ```bash
-bands.x < si_bands_pp.in > si_bands_pp.out
+bands.x < pp.bands.silicon.in > pp.bands.silicon.out
 ```
 
 Finally, we run `plotband.x` to visualize bandstructure. We can either run it

docs/hands-on/convergence.mdx

@@ -25,7 +25,7 @@ Now we can plot the total energy with respect to ecutwfc. The data is in
 
 We will use matplotlib to make the plots. Here is the python code for plotting:
 
-```python title="notebooks/si-plots.ipynb" showLineNumbers
+```python title="notebooks/silicon-scf.ipynb" showLineNumbers
 import matplotlib.pyplot as plt
 from matplotlib import rcParamsDefault
 import numpy as np

docs/hands-on/dos.mdx

@@ -21,7 +21,7 @@ of DOS depends on the integration in $k$ space.
 3. Finally, the DOS can be determined by integrating the electron density in $k$
 space.
 
-I have created a new input file (`si_scf_dos.in`) which is very much the same as
+I have created a new input file (`pw.scf.silicon_dos.in`) which is very much the same as
 our previous scf input file except some parameters are modified. You can find
 all the input files in my [GitHub repository](
 https://github.com/pranabdas/espresso/). We used the lattice constant value that
@@ -31,7 +31,7 @@ pseudo-potential, it might result stress in the system. We have increased the
 `ecutwfc` to have better precision. We run the scf calculation:
 
 ```bash
-pw.x < si_scf_dos.in > si_scf_dos.out
+pw.x < pw.scf.silicon_dos.in > pw.scf.silicon_dos.out
 ```
 
 Next, we have prepared the input file for the `nscf` calculation. Where is have
@@ -46,21 +46,21 @@ Kohn-Sham states.
 
 
 ```bash
-pw.x < si_nscf_dos.in > si_nscf_dos.out
+pw.x < pw.nscf.silicon_dos.in > pw.nscf.silicon_dos.out
 ```
 
 Now our final step is to calculate the density of states. The DOS input file as
 follows:
 
 import CodeBlock from '@theme/CodeBlock';
-import si_dos_in from '!!raw-loader!/src/silicon/si_dos.in';
+import si_dos_in from '!!raw-loader!/src/silicon/pp.dos.silicon.in';
 
-<CodeBlock language="bash" title="src/silicon/si_dos.in" showLineNumbers>{si_dos_in}</CodeBlock>
+<CodeBlock language="bash" title="src/silicon/pp.dos.silicon.in" showLineNumbers>{si_dos_in}</CodeBlock>
 
 We run:
 
 ```bash
-dos.x < si_dos.in > si_dos.out
+dos.x < pp.dos.silicon.in > pp.dos.silicon.out
 ```
 
 The DOS data in the `si_dos.dat` file that we specified in our input file. We

docs/hands-on/scf.mdx

@@ -64,7 +64,7 @@ have to provide the full path where the `pw.x` executable is located.
 
 :::
 
-Now let’s look at the output file `pw.scf.silicon.out` and see how the
+Now let's look at the output file `pw.scf.silicon.out` and see how the
 convergence is reached:
 
 ```bash

src/silicon/si_bands.in → src/silicon/pw.bands.silicon.in

@@ -3,7 +3,7 @@
   restart_mode = 'from_scratch',
   prefix = 'silicon',
   outdir = './tmp/'
-  pseudo_dir = './pseudos/'
+  pseudo_dir = '../pseudos/'
   verbosity = 'high'
 /
 

src/silicon/si_nscf_dos.in → src/silicon/pw.nscf.silicon_dos.in

@@ -3,7 +3,7 @@
   restart_mode = 'from_scratch',
   prefix = 'silicon',
   outdir = './tmp/'
-  pseudo_dir = './pseudos/'
+  pseudo_dir = '../pseudos/'
   verbosity = 'high'
 /
 

src/silicon/si_bands_scf.in → src/silicon/pw.scf.silicon_bands.in

@@ -3,7 +3,7 @@
   restart_mode = 'from_scratch',
   prefix = 'silicon',
   outdir = './tmp/'
-  pseudo_dir = './pseudos/'
+  pseudo_dir = '../pseudos/'
   verbosity = 'high'
 /
 

src/silicon/si_scf_dos.in → src/silicon/pw.scf.silicon_dos.in

@@ -3,7 +3,7 @@
   restart_mode = 'from_scratch',
   prefix = 'silicon',
   outdir = './tmp/'
-  pseudo_dir = './pseudos/'
+  pseudo_dir = '../pseudos/'
   verbosity = 'high'
 /