Updated tutorial 4 to use new markdown output

docs/_static/tutorials/fetch.py

@@ -61,6 +61,9 @@ def extract(filename_in, filename_out, start=0, end=None, heading=None):
     extract('../../../tutorials/tutorial_3/01-ki/zno.md', 'tutorial_3/md_excerpts/zno_ham.md', -3, -2)
     copy('../../../tutorials/tutorial_3/01-ki/01-koopmans-dfpt/Koopmans_DFPT_bandstructure.png', 'tutorial_3/')
 
+    # Tutorial 4
+    extract('../../../tutorials/tutorial_4/h2o_conv.md', 'tutorial_4/md_excerpts/h2o_conv.md', 18, 36)
+
     # Tutorial 5
     extract('../../../tutorials/tutorial_5/01-train/h2o_train.md', 'tutorial_5/md_excerpts/train.md', 45, 92)
     extract('../../../tutorials/tutorial_5/02-predict/h2o_predict.md',

docs/_static/tutorials/tutorial_4/md_excerpts/h2o_conv.md

@@ -0,0 +1,18 @@
+- **Singlepoint ecutwfc 20_0 celldm1 11_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  
+- **Singlepoint ecutwfc 20_0 celldm1 12_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  
+- **Singlepoint ecutwfc 20_0 celldm1 13_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  
+- **Singlepoint ecutwfc 30_0 celldm1 11_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  
+- **Singlepoint ecutwfc 30_0 celldm1 12_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  
+- **Singlepoint ecutwfc 30_0 celldm1 13_3**
+  - **DFTCP**
+    - ✅ `01-dft` completed  

docs/tutorials/tutorial_4.rst

@@ -27,9 +27,12 @@ The output file
 '''''''''''''''
 When you run the calculation, you should see something like this after the header:
 
-.. literalinclude:: ../../tutorials/tutorial_4/h2o_conv.log
-  :lines: 15-34
-  :language: text
+----
+
+.. include:: ../_static/tutorials/tutorial_4/md_excerpts/h2o_conv.md
+  :parser: myst_parser.sphinx_
+
+----
 
 Here, the code is attempting to use progressively larger energy cutoffs and cell sizes. It will ultimately arrive at a converged solution, with a ``ecutwfc`` of 50.0 Ha and a cell slightly larger than that provided in the ``.json`` input file.
 
@@ -58,9 +61,9 @@ Hopefully, the first thing you will see is that there are now some warnings abou
 
 .. code-block:: text
 
-  UserWarning: Small box parameters "nrb" not provided in input: these will be automatically set to safe default values. These values can probably be decreased, but this would require convergence tests.
-  Estimated real mesh dimension (nr1, nr2, nr3) = ...
-  Small box mesh dimension (nr1b, nr2b, nr3b) = ...
+  🚨 Small box parameters `nrb` not provided in input: these will be automatically set to safe default values. These 
+  values can probably be decreased, but this would require convergence tests. Estimated real mesh dimension `(nr1, 
+  nr2, nr3) = 36 36 45`. Small box mesh dimension `(nr1b, nr2b, nr3b) = 20 18 20`.
 
 These parameters are associated with the way ``Quantum ESPRESSO`` handles non-local core corrections in pseudopotentials, and corrections are present in the new set of pseudopotentials but absent in the SG15 pseudopotentials.
 
@@ -71,4 +74,4 @@ So, let's perform a convergence test! The ``nrb`` parameters are not directly im
 Running this script will perform a convergence test with respect to ``nrb 1-3``.
 
 .. warning:: 
-  This tutorial performs convergence tests in a slightly incorrect way, To see this, add the keyword ``length = 10`` to the ``ConvergenceVarialbe`` in the above script. How is the behaviour different? Which behaviour is correct? Why?
+  This tutorial performs convergence tests in a slightly incorrect way, To see this, add the keyword ``length = 10`` to the ``ConvergenceVariable`` in the above script. How is the behavior different? Which behavior is correct? Why?

tutorials/tutorial_4/custom_convergence.py

@@ -36,9 +36,7 @@ def set_nrb(workflow, value):
                                              get_value=get_nrb,
                                              set_value=set_nrb)
 
-# Create the convergence workflow using the convergence factory. Because koopmans knows how to
-# converge with respect to ecutwfc, we don't need to implement a custom ConvergenceVariable for it
-# and instead can just tell it the variable name
+# Create the convergence workflow using the convergence factory
 workflow = workflows.ConvergenceWorkflowFactory(subworkflow,
                                                 observable='total energy',
                                                 threshold=1e-3,

tutorials/tutorial_4/h2o_conv.md

@@ -0,0 +1,108 @@
+
+  koopmans
+  ========
+
+  *Koopmans spectral functional calculations with `Quantum ESPRESSO`*
+
+  📦 **Version:** 1.1.0  
+  🧑 **Authors:** Edward Linscott, Nicola Colonna, Riccardo De Gennaro, Ngoc Linh Nguyen, Giovanni Borghi, Andrea 
+  Ferretti, Ismaila Dabo, and Nicola Marzari  
+  📚 **Documentation:** https://koopmans-functionals.org  
+  ❓ **Support:** https://groups.google.com/g/koopmans-users  
+  🐛 **Report a bug:** https://github.com/epfl-theos/koopmans/issues/new
+
+  > [!NOTE]  
+  > Please cite the papers listed in `h2o_conv.bib` in work involving this calculation
+
+  h2o_conv
+  --------
+  - **Singlepoint ecutwfc 20_0 celldm1 11_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 20_0 celldm1 12_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 20_0 celldm1 13_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 30_0 celldm1 11_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 30_0 celldm1 12_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 30_0 celldm1 13_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 40_0 celldm1 11_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 40_0 celldm1 12_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 40_0 celldm1 13_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+
+Progress update
+  ecutwfc still appears unconverged, will reattempt using a finer value
+  celldm1 still appears unconverged, will reattempt using a finer value
+
+  - **Singlepoint ecutwfc 20_0 celldm1 14_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 30_0 celldm1 14_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 40_0 celldm1 14_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 50_0 celldm1 11_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 50_0 celldm1 12_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 50_0 celldm1 13_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 50_0 celldm1 14_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+
+Progress update
+  ecutwfc appears converged
+  celldm1 appears converged
+  ... but the variables are not collectively converged. Cautiously incrementing all variables.
+
+  - **Singlepoint ecutwfc 20_0 celldm1 15_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 30_0 celldm1 15_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 40_0 celldm1 15_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 50_0 celldm1 15_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 60_0 celldm1 11_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 60_0 celldm1 12_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 60_0 celldm1 13_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 60_0 celldm1 14_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+  - **Singlepoint ecutwfc 60_0 celldm1 15_3**
+    - **DFTCP**
+      - ✅ `01-dft` completed  
+
+   Converged variables are ecutwfc = 50.0, celldm1 = 13.33835675502157
+
+  **Workflow complete** 🎉