Refactor to run all calculations in separate directories

.github/workflows/tests.yml

@@ -21,10 +21,10 @@ jobs:
            uses: actions/checkout@v3
            with:
               submodules: true
-         - name: Set up Python 3.8
+         - name: Set up Python
            uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip

.github/workflows/tutorials.yml

@@ -21,10 +21,10 @@ jobs:
            uses: actions/checkout@v3
            with:
               submodules: true
-         - name: Set up Python 3.8
+         - name: Set up Python
            uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip

.github/workflows/typechecking.yml

@@ -19,10 +19,10 @@ jobs:
            uses: actions/checkout@v3
            with:
               submodules: false
-         - name: Set up Python 3.8
+         - name: Set up Python
            uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip

.github/workflows/update_citation.yml

@@ -17,10 +17,10 @@ jobs:
          - name: Get branch name
            id: branch-name
            uses: tj-actions/branch-names@v8
-         - name: Set up Python 3.8
+         - name: Set up Python
            uses: actions/setup-python@v4
            with:
-              python-version: 3.8
+              python-version: '3.10'
          - name: Install dependencies
            run: |
               python -m pip install --upgrade pip
@@ -30,7 +30,9 @@ jobs:
            run: |
               python bin/update_cff.py
          - name: Validate CITATION.cff
-           uses: dieghernan/cff-validator@main
+           uses: dieghernan/cff-validator@v3
+           with:
+             install-r: true
          - name: Commit changes
            uses: test-room-7/action-update-file@v1
            with:

.gitignore

@@ -17,15 +17,6 @@ coverage.xml
 .mypy_cache/
 TMP-CP/
 TMP/
-calc_alpha/
-calculate_eps/
-dft_bands/
-final/
-init/
-pdos/
-postproc/
-wannier/
-screening/
-hamiltonian/
+??-*/
 build/
 dist/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
         types: [file, python]
@@ -16,14 +16,14 @@ repos:
       - id: isort
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: src/koopmans/
         args: [--ignore-missing-imports]
 
   - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.6.0
+    rev: v2.0.4
     hooks:
     - id: autopep8
       args: [--max-line-length=120, -i]

CITATION.cff

@@ -71,4 +71,4 @@ preferred-citation:
 repository-code: https://github.com/epfl-theos/koopmans/
 title: koopmans
 type: software
-version: 1.0.1
+version: 1.1.0

bin/update_cff.py

@@ -1,5 +1,7 @@
 import sys
+
 import yaml
+
 if sys.version_info >= (3, 8):
     from importlib import metadata
 else:

docs/_static/tutorials/fetch.py

@@ -0,0 +1,71 @@
+from shutil import copy
+
+
+def extract(filename_in, filename_out, start=0, end=None, heading=None):
+    with open(filename_in) as fd:
+        flines = fd.readlines()
+
+    # If heading is provided, find the line number of the heading
+    if heading:
+        for i, line in enumerate(flines):
+            if heading in line:
+                start = i
+                break
+        else:
+            raise ValueError(f'Heading {heading} not found in file {filename_in}')
+
+        indent = len(flines[start]) - len(flines[start].lstrip())
+
+        for i in range(start + 1, len(flines)):
+            line = flines[i]
+            if not line.startswith(' ' * (indent + 1)):
+                end = i
+                break
+        else:
+            raise ValueError(f'Could not find the end of the {heading} block')
+
+    flines = flines[start:end]
+
+    # Find the shortest leading whitespace and strip this from all lines (as otherwise the markdown will be rendered as a code block)
+    min_indent = min(len(line) - len(line.lstrip()) for line in flines if line.strip())
+    flines = [line if line == "\n" else line[min_indent:]for line in flines]
+
+    # Manual conversion of double spaces to /
+    flines = [line[:-2] + '\ \n' if (line.endswith('  \n')
+                                     and not line.strip().startswith('-')) else line for line in flines]
+
+    with open(filename_out, 'w') as fd:
+        fd.writelines(flines)
+
+
+if __name__ == '__main__':
+    # Tutorial 1
+    extract('../../../tutorials/tutorial_1/ozone.md', 'tutorial_1/md_excerpts/ozone_init.md', heading='Initialization')
+    extract('../../../tutorials/tutorial_1/ozone.md', 'tutorial_1/md_excerpts/ozone_alpha.md', 24, 33)
+    extract('../../../tutorials/tutorial_1/ozone.md', 'tutorial_1/md_excerpts/ozone_alpha_10.md', 45, 49)
+    extract('../../../tutorials/tutorial_1/ozone.md', 'tutorial_1/md_excerpts/ozone_tables.md', 50, 62)
+    extract('../../../tutorials/tutorial_1/ozone.md', 'tutorial_1/md_excerpts/ozone_final.md', -4)
+
+    # Tutorial 2
+    extract('../../../tutorials/tutorial_2/si_wannierize.md', 'tutorial_2/md_excerpts/si_wannierize.md', start=18)
+    extract('../../../tutorials/tutorial_2/si_ki.md', 'tutorial_2/md_excerpts/si_ki_wannierize.md', heading="Wannierize")
+    extract('../../../tutorials/tutorial_2/si_ki.md', 'tutorial_2/md_excerpts/si_ki_fold.md', heading="Fold To Supercell")
+    extract('../../../tutorials/tutorial_2/si_ki.md', 'tutorial_2/md_excerpts/si_ki_screening.md', 51, 61)
+    extract('../../../tutorials/tutorial_2/si_ki.md',
+            'tutorial_2/md_excerpts/si_ki_postproc.md', heading="Unfold And Interpolate")
+
+    # Tutorial 3
+    extract('../../../tutorials/tutorial_3/01-ki/zno.md',
+            'tutorial_3/md_excerpts/zno_wannierize_section.md', heading='Wannierize')
+    extract('../../../tutorials/tutorial_3/01-ki/zno.md', 'tutorial_3/md_excerpts/zno_w2kc.md', -4, -3)
+    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',
+            'tutorial_5/md_excerpts/predict.md', heading='Calculate Screening Via DSCF')
+    extract('../../../tutorials/tutorial_5/03-test/h2o_test.md', 'tutorial_5/md_excerpts/test.md', 45, 96)

docs/_static/tutorials/tutorial_1/md_excerpts/ozone_alpha.md

@@ -0,0 +1,9 @@
+- **Calculate Screening Via DSCF**
+  - **Iteration 1**
+    - ✅ `01-ki` completed  
+    - **Orbital 1**
+      - ✅ `01-dft_n-1` completed  
+    - **Orbital 2**
+      - ✅ `01-dft_n-1` completed  
+    - **Orbital 3**
+      - ✅ `01-dft_n-1` completed  

docs/_static/tutorials/tutorial_1/md_excerpts/ozone_alpha_10.md

@@ -0,0 +1,4 @@
+- **Orbital 10**
+  - ✅ `01-dft_n+1_dummy` completed  
+  - ✅ `02-pz_print` completed  
+  - ✅ `03-dft_n+1` completed  

docs/_static/tutorials/tutorial_1/md_excerpts/ozone_final.md

@@ -0,0 +1,4 @@
+
+  - ✅ `03-ki_final` completed  
+
+**Workflow complete** 🎉

docs/_static/tutorials/tutorial_1/md_excerpts/ozone_init.md

@@ -0,0 +1,5 @@
+- **Initialization**
+  - ✅ `01-dft_init_nspin1` completed  
+  - ✅ `02-dft_init_nspin2_dummy` completed  
+  - ✅ `03-convert_files_from_spin1to2` completed  
+  - ✅ `04-dft_init_nspin2` completed  

docs/_static/tutorials/tutorial_1/md_excerpts/ozone_tables.md

@@ -0,0 +1,12 @@
+**α**
+|    |        1 |        2 |       3 |        4 |        5 |        6 |        7 |        8 |        9 |       10 |
+|---:|---------:|---------:|--------:|---------:|---------:|---------:|---------:|---------:|---------:|---------:|
+|  0 | 0.6      | 0.6      | 0.6     | 0.6      | 0.6      | 0.6      | 0.6      | 0.6      | 0.6      | 0.6      |
+|  1 | 0.655691 | 0.727571 | 0.78386 | 0.663859 | 0.772354 | 0.726848 | 0.729968 | 0.741899 | 0.779264 | 0.717389 |
+
+**ΔE<sub>i</sub> - λ<sub>ii</sub> (eV)**
+|    |        1 |         2 |        3 |         4 |        5 |         6 |         7 |         8 |        9 |       10 |
+|---:|---------:|----------:|---------:|----------:|---------:|----------:|----------:|----------:|---------:|---------:|
+|  0 | -0.47736 | -0.920499 | -1.12409 | -0.452149 | -1.05055 | -0.830893 | -0.785139 | -0.888597 | -1.05016 | 0.711209 |
+
+

docs/_static/tutorials/tutorial_2/md_excerpts/si_ki_fold.md

@@ -0,0 +1,3 @@
+- **Fold To Supercell**
+  - ✅ `01-convert_block_1_to_supercell` completed  
+  - ✅ `02-convert_block_2_to_supercell` completed  

docs/_static/tutorials/tutorial_2/md_excerpts/si_ki_postproc.md

@@ -0,0 +1,16 @@
+- **Unfold And Interpolate**
+  - **Wannierize**
+    - ✅ `01-scf` completed  
+    - ✅ `02-nscf` completed  
+    - **Wannierize Block 1**
+      - ✅ `01-wannier90_preproc` completed  
+      - ✅ `02-pw2wannier90` completed  
+      - ✅ `03-wannier90` completed  
+    - **Wannierize Block 2**
+      - ✅ `01-wannier90_preproc` completed  
+      - ✅ `02-pw2wannier90` completed  
+      - ✅ `03-wannier90` completed  
+    - ✅ `05-bands` completed  
+    - ✅ `06-projwfc` completed  
+  - ✅ `02-unfold_and_interpolate_occ` completed  
+  - ✅ `03-unfold_and_interpolate_emp` completed  

docs/_static/tutorials/tutorial_2/md_excerpts/si_ki_screening.md

@@ -0,0 +1,10 @@
+- **Calculate Screening Via DSCF**
+  - **Iteration 1**
+    - ✅ `01-ki` completed  
+    - **Orbital 32**
+      - ✅ `01-dft_n-1` completed  
+    - **Orbital 33**
+      - ✅ `01-dft_n+1_dummy` completed  
+      - ✅ `02-pz_print` completed  
+      - ✅ `03-dft_n+1` completed  
+

docs/_static/tutorials/tutorial_2/md_excerpts/si_ki_wannierize.md

@@ -0,0 +1,11 @@
+- **Wannierize**
+  - ✅ `01-scf` completed  
+  - ✅ `02-nscf` completed  
+  - **Wannierize Block 1**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - **Wannierize Block 2**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  

docs/_static/tutorials/tutorial_2/md_excerpts/si_wannierize.md

@@ -0,0 +1,14 @@
+- ✅ `01-scf` completed  
+- ✅ `02-nscf` completed  
+- **Wannierize Block 1**
+  - ✅ `01-wannier90_preproc` completed  
+  - ✅ `02-pw2wannier90` completed  
+  - ✅ `03-wannier90` completed  
+- **Wannierize Block 2**
+  - ✅ `01-wannier90_preproc` completed  
+  - ✅ `02-pw2wannier90` completed  
+  - ✅ `03-wannier90` completed  
+- ✅ `05-bands` completed  
+- ✅ `06-projwfc` completed  
+
+**Workflow complete** 🎉

docs/_static/tutorials/tutorial_3/md_excerpts/zno_ham.md

@@ -0,0 +1 @@
+- ✅ `03-kc_ham` completed  

docs/_static/tutorials/tutorial_3/md_excerpts/zno_w2kc.md

@@ -0,0 +1 @@
+- ✅ `02-wann2kc` completed  

docs/_static/tutorials/tutorial_3/md_excerpts/zno_wannierize_section.md

@@ -0,0 +1,28 @@
+- **Wannierize**
+  - ✅ `01-scf` completed  
+  - ✅ `02-nscf` completed  
+  - **Wannierize Block 1**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - **Wannierize Block 2**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - **Wannierize Block 3**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - **Wannierize Block 4**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - **Wannierize Block 5**
+    - ✅ `01-wannier90_preproc` completed  
+    - ✅ `02-pw2wannier90` completed  
+    - ✅ `03-wannier90` completed  
+  - ✅ `08-merge_occ_wannier_hamiltonian` completed  
+  - ✅ `09-merge_occ_wannier_u` completed  
+  - ✅ `10-merge_occ_wannier_centers` completed  
+  - ✅ `11-bands` completed  
+  - ✅ `12-projwfc` completed  

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/_static/tutorials/tutorial_5/md_excerpts/predict.md

@@ -0,0 +1,19 @@
+- **Calculate Screening Via DSCF**
+  - **Iteration 1**
+    - ✅ `01-ki` completed  
+    - **Power Spectrum Decomposition**
+      - **Convert Orbital Files To XML**
+        - ✅ `01-bin2xml_total_density` completed  
+        - ✅ `02-bin2xml_occ_spin_0_orb_1_density` completed  
+        - ✅ `03-bin2xml_occ_spin_0_orb_2_density` completed  
+        - ✅ `04-bin2xml_occ_spin_0_orb_3_density` completed  
+        - ✅ `05-bin2xml_occ_spin_0_orb_4_density` completed  
+        - ✅ `06-bin2xml_emp_spin_0_orb_5_density` completed  
+        - ✅ `07-bin2xml_emp_spin_0_orb_6_density` completed  
+      - ✅ `02-extract_coefficients_from_xml` completed  
+      - ✅ `03-compute_power_spectrum_orbital_1` completed  
+      - ✅ `04-compute_power_spectrum_orbital_2` completed  
+      - ✅ `05-compute_power_spectrum_orbital_3` completed  
+      - ✅ `06-compute_power_spectrum_orbital_4` completed  
+      - ✅ `07-compute_power_spectrum_orbital_5` completed  
+      - ✅ `08-compute_power_spectrum_orbital_6` completed