add workflow links to mat3ra

docs/hands-on/bands.mdx

@@ -3,19 +3,23 @@ title: Bandstructure Calculation
 sidebar_label: Bandstructure
 ---
 
+import Mat3raAdmonition from '../../src/apps/mat3ra';
+
+<Mat3raAdmonition url="https://platform.mat3ra.com/seminar/projects/seminar-espresso-tutorials/jobs/DgNA7K8o46K6CTM6W" />
+
 Before we can run `bands` calculation, we need to perform single-point [self
 consistent field calculation](scf.mdx). 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 +37,28 @@ 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/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
@@ -31,9 +31,13 @@ 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
 ```
 
+import Mat3raAdmonition from '../../src/apps/mat3ra';
+
+<Mat3raAdmonition url="https://platform.mat3ra.com/seminar/projects/seminar-espresso-tutorials/jobs/6XhvtFpEc7kmwK5Q3" />
+
 Next, we have prepared the input file for the `nscf` calculation. Where is have
 added `occupations` in the `&system` card as `tetrahedra` (appropriate for DOS
 calculation). We have increased the number of k-points to 12 × 12 × 12 with
@@ -46,21 +50,21 @@ 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

@@ -36,6 +36,10 @@ lines can be added with lines starting with a `!` like in Fortran. Also,
 parameter names are not case-sensitive, i.e., `&control` and `&CONTROL` are the
 same.
 
+import ColabBadge from '../../src/apps/colab';
+
+<ColabBadge notebook="silicon-scf.ipynb" />
+
 import CodeBlock from '@theme/CodeBlock';
 import pw_scf_silicon_in from '!!raw-loader!/src/silicon/pw.scf.silicon.in';
 

docs/hands-on/wannier.mdx

@@ -6,7 +6,7 @@ title: Wannier method
 
 1. Perform `scf` calculation using Quantum Espresso `pw.x`
 
-```console
+```bash
 QE_PATH="/workspaces/q-e-qe-7.2/bin"
 mpirun -np 4 ${QE_PATH}/pw.x -i pw.scf.silicon.in > pw.scf.silicon.out
 ```
@@ -15,42 +15,42 @@ mpirun -np 4 ${QE_PATH}/pw.x -i pw.scf.silicon.in > pw.scf.silicon.out
 to provide explicit list of k-points. Such explicit list of k-points can be
 generated using perl script included in the Wannier package under utility.
 
-```console
+```bash
 WANNIER_PATH="/workspaces/wannier90-3.1.0"
 # directly append the k-points to the input file
 ${WANNIER_PATH}/utility/kmesh.pl 4 4 4 >> pw.nscf.silicon.in
 ```
 
 Run `nscf` calculation:
 
-```console
+```bash
 mpirun -np 4 ${QE_PATH}/pw.x -i pw.nscf.silicon.in > pw.nscf.silicon.out
 ```
 
 3. Prepare input file for wannier90 (`silicon.win`). Here we need the k-points
 list without the weights:
 
-```console
+```bash
 ${WANNIER_PATH}/utility/kmesh.pl 4 4 4 wan
 ```
 
 4. Generate nnkp input:
 
-```console
+```bash
 # we can just provide the seedname or seedname.win
 ${WANNIER_PATH}/wannier90.x -pp silicon
 ```
 
 5. Create input file for `pw2wan`, and generate initial projections:
 
-```console
+```bash
 mpirun -np 4 ${WANNIER_PATH}/pw2wannier90.x -i pw2wan.silicon.in > pw2
 wan.silicon.out
 ```
 
 6. Run wannier calculation:
 
-```console
+```bash
 mpirun -np 4 ${WANNIER_PATH}/wannier90.x silicon
 ```