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Merged
AsymmetryChou merged 9 commits into from
Sep 26, 2025
Merged

Update tutorial 2 and add it to index.rst #40

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cfd4a99
add self-enrgy for k20 in .gitignore
AsymmetryChou Sep 23, 2025
79aed84
add tutor2 in index.rst
AsymmetryChou Sep 23, 2025
0e56c4a
add hBN and MoS2
AsymmetryChou Sep 25, 2025
8494259
add MoS2
AsymmetryChou Sep 26, 2025
89051d8
add MoS2 model
AsymmetryChou Sep 26, 2025
4bab7f3
add hBN model
AsymmetryChou Sep 26, 2025
830bea6
add hBN TBT results
AsymmetryChou Sep 26, 2025
0ba2cfb
update tutor2
AsymmetryChou Sep 26, 2025
0691d17
add docs
AsymmetryChou Sep 26, 2025
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10 changes: 8 additions & 2 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,14 @@ dpnegf/negf/check.ipynb
dpnegf/tests/data/test_negf/show.ipynb
dpnegf/tests/data/test_tbtrans/show.ipynb
# tutorial files
dpnegf/examples/graphene/negf_output_k20/self_energy/self_energy_leadL.h5
dpnegf/examples/graphene/negf_output_k20/self_energy/self_energy_leadR.h5
examples/graphene/negf_output_k20/self_energy/self_energy_leadL.h5
examples/graphene/negf_output_k20/self_energy/self_energy_leadR.h5
examples/hBN/negf_output_k20/self_energy/self_energy_leadL.h5
examples/hBN/negf_output_k20/self_energy/self_energy_leadR.h5
examples/hBN/negf_output_k50/self_energy/*
examples/hBN/negf_output_k70/self_energy/*



run_config.json
dpnegf/nnet/__pycache__/
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1 change: 1 addition & 0 deletions docs/hands_on/index.rst
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Expand Up @@ -4,3 +4,4 @@ A quick Example

.. toctree::
tutorial1_c_chain
tutorial2_2d_mat
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@coderabbitai coderabbitai Bot Sep 26, 2025

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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

Confirm toctree target exists

Please confirm that docs/hands_on/tutorial2_2d_mat.rst (or matching path) is present; otherwise the Sphinx build will emit a “document not found” warning.

Run this to double-check the file is there:

🏁 Script executed:

#!/bin/bash
fd tutorial2_2d_mat.rst docs

Length of output: 0

🏁 Script executed:

#!/bin/bash
set -e
echo "Listing .rst files in docs/hands_on:"
fd -e rst docs/hands_on
echo
echo "Searching for 'tutorial2_2d_mat' in all .rst under docs:"
rg -l 'tutorial2_2d_mat' -g '*.rst' docs || true

Length of output: 394

🏁 Script executed:

#!/bin/bash
set -e
echo "Listing all .rst files in docs/hands_on:"
find docs/hands_on -maxdepth 1 -type f -name '*.rst' || echo "No .rst files found in docs/hands_on"

echo
echo "Searching for tutorial2_2d_mat.rst anywhere under docs:"
find docs -type f -name 'tutorial2_2d_mat.rst' || echo "tutorial2_2d_mat.rst not found"

Length of output: 121

Confirm toctree target exists
docs/hands_on/tutorial2_2d_mat.rst not found; add the missing file or update the toctree entry at docs/hands_on/index.rst:7 to reference an existing document.

🤖 Prompt for AI Agents 
In docs/hands_on/index.rst around line 7 the toctree entry "tutorial2_2d_mat"
points to a non-existent file; either add a new file at
docs/hands_on/tutorial2_2d_mat.rst with the intended content, or update the
toctree entry to reference the correct existing document name/path (matching the
actual .rst filename without extension). After updating, ensure the referenced
file is committed and run a local Sphinx build to confirm the toctree resolves.

1,647 changes: 1,615 additions & 32 deletions docs/hands_on/tutorial2_2d_mat.ipynb
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14 changes: 14 additions & 0 deletions examples/MoS2/MoS2_orth.vasp
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@@ -0,0 +1,14 @@
MoS2
1.0
3.1912000179 0.0000000000 0.0000000000
0.0000000000 18.1270999908 0.0000000000
0.0000000000 0.0000000000 5.5272998810
Mo S
2 4
Cartesian
0.000000000 9.063549995 0.000000000
1.595600009 9.063549995 2.763649940
0.000000000 10.633718911 1.842414899
1.595600009 10.633718911 4.606064675
0.000000000 7.493380540 1.842414899
1.595600009 7.493380540 4.606064675
11 changes: 11 additions & 0 deletions examples/MoS2/POSCAR
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@@ -0,0 +1,11 @@
Mo S
1.0000000000000000
3.1911949999999996 0.0000000000000000 0.0000000000000000
-1.5955980000000001 2.7636560000000001 0.0000000000000000
-0.0000000000000000 -0.0000000000000000 18.1271099999999983
Mo S
1 2
Cartesian
0.0000000000000000 0.0000000000000000 9.0635549999999991
1.5955989289309997 0.9212177454480001 10.6337615224199986
1.5955989289309997 0.9212177454480001 7.4933484775799997
16 changes: 16 additions & 0 deletions examples/MoS2/extra_baseline/MoS_spds.json
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{
"common_options": {
"basis": {
"Mo": [
"5s",
"5p",
"4d"
],
"S": [
"3s",
"3p",
"d*"
]
}
}
}
93 changes: 93 additions & 0 deletions examples/MoS2/extra_baseline/input_templete.json
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{
"common_options": {
"basis": {
"Mo": [
"5s",
"5p",
"4d"
],
"S": [
"3s",
"3p",
"d*"
]
},
"device": "cpu",
"dtype": "float32",
"overlap": true,
"seed": 3982377700
},
"train_options": {
"num_epoch": 2,
"batch_size": 1,
"optimizer": {
"lr": 0.01,
"type": "Adam"
},
"lr_scheduler": {
"type": "exp",
"gamma": 0.999
},
"loss_options": {
"train": {
"method": "eigvals",
"diff_on": false,
"eout_weight": 0.001,
"diff_weight": 0.01
}
},
"save_freq": 1,
"validation_freq": 10,
"display_freq": 100,
"ref_batch_size": 1,
"val_batch_size": 1,
"max_ckpt": 4
},
"model_options": {
"nnsk": {
"onsite": {
"method": "uniform"
},
"hopping": {
"method": "poly4pow",
"rs": {
"S-S": 5.66,
"S-Mo": 5.85,
"Mo-S": 5.85,
"Mo-Mo": 6.03
},
"w": 0.2
},
"soc": {},
"freeze": [
"overlap"
],
"push": false,
"std": 0.01,
"atomic_radius": "cov"
}
},
"data_options": {
"train": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"validation": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"reference": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
}
Comment on lines +71 to +91
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@coderabbitai coderabbitai Bot Sep 26, 2025

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⚠️ Potential issue | 🟠 Major

Point the template to the committed MoS₂ dataset

With root still set to "path/to/dataset" and the placeholder "prexfix_for_dataset", anyone trying to run this “baseline” straight from the repo will immediately hit a FileNotFoundError because the loader can’t locate the data you added under examples/MoS2/train/data. Let’s wire the template to that dataset (both for train/val/reference) so the example actually runs out of the box.

-            "root": "path/to/dataset",
-            "prefix": "prexfix_for_dataset",
+            "root": "../train/data",
+            "prefix": "kpath.0",

Repeat the same adjustment for the validation and reference sections.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
"train": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"validation": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"reference": {
"root": "path/to/dataset",
"prefix": "prexfix_for_dataset",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
}
"train": {
"root": "../train/data",
"prefix": "kpath.0",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"validation": {
"root": "../train/data",
"prefix": "kpath.0",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
},
"reference": {
"root": "../train/data",
"prefix": "kpath.0",
"get_eigenvalues": true,
"type": "DefaultDataset",
"get_Hamiltonian": false
}
🤖 Prompt for AI Agents 
In examples/MoS2/extra_baseline/input_templete.json around lines 71-91 the
dataset paths are placeholders ("path/to/dataset" and "prexfix_for_dataset")
which will cause FileNotFoundError; update the "root" values to point to the
committed example dataset directory (examples/MoS2/train/data) and set the
"prefix" to the actual prefix used by those files for the train, validation, and
reference sections so the example runs out-of-the-box.

}
}
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