feature/SOF-8072 Feature: SE for a Ti adatom on a 5×5 TiN island, descent energetics of Fig. 6 (MACE and DFT) - #385

python3 - <<'PY'
import json
from pathlib import Path

nb = Path("other/materials_designer/specific_examples/defect_surface_island_titanium_nitride_SIMULATION.ipynb")
data = json.loads(nb.read_text())
for i, cell in enumerate(data.get("cells", [])):
    src = "".join(cell.get("source", []))
    if "apply_all_patches" in src or "is_pyodide_environment" in src:
        print(f"NOTEBOOK CELL {i} ({cell.get('cell_type')}):")
        print(src)

for p in [
    Path("src/py/mat3ra/notebooks_utils/pyodide/packages/patches.py"),
    Path("src/py/mat3ra/notebooks_utils/primitive/environment.py"),
]:
    print(f"\n--- {p} ---")
    if p.exists():
        lines = p.read_text().splitlines()
        for n, line in enumerate(lines, 1):
            if ("def apply_all_patches" in line or
                "mace" in line.lower() or
                "torch.linalg" in line or
                "def is_pyodide_environment" in line):
                lo = max(1, n - 8)
                hi = min(len(lines), n + 25)
                for k in range(lo, hi + 1):
                    print(f"{k:4}: {lines[k-1]}")
                print()
    else:
        print("MISSING")
PY

python3 - <<'PY'
from pathlib import Path

for p in [
    Path("src/py/mat3ra/notebooks_utils/pyodide/packages/torch.py"),
    Path("src/py/mat3ra/notebooks_utils/pyodide/packages/mace.py"),
]:
    print(f"--- {p} ---")
    if not p.exists():
        print("MISSING")
        continue
    lines = p.read_text().splitlines()
    for n, line in enumerate(lines, 1):
        print(f"{n:4}: {line}")
PY

python3 - <<'PY'
import json
from pathlib import Path

nb = Path("other/materials_designer/specific_examples/defect_surface_island_titanium_nitride_SIMULATION.ipynb")
data = json.loads(nb.read_text())
terms = (
    "Run All", "native", "create_mace_calculator", "MACECalculator",
    "mace_mp", "BFGS", "optimize", "get_forces", "calculate_total_energy",
    "relax", "apply_all_patches"
)
for i, cell in enumerate(data.get("cells", [])):
    src = "".join(cell.get("source", []))
    if any(t.lower() in src.lower() for t in terms):
        print(f"\n--- NOTEBOOK CELL {i} ({cell.get('cell_type')}) ---")
        print(src)

print("\n--- repository references to patched linalg and MACE execution ---")
for root in ["src/py", "other/materials_designer"]:
    for p in sorted(Path(root).rglob("*")):
        if p.suffix not in {".py", ".ipynb"}:
            continue
        try:
            text = p.read_text()
        except Exception:
            continue
        hits = []
        for n, line in enumerate(text.splitlines(), 1):
            if any(term.lower() in line.lower() for term in (
                "torch.linalg", "create_mace_calculator", "MACECalculator", "mace_mp"
            )):
                hits.append((n, line))
        if hits:
            print(f"\n{p}")
            for n, line in hits[:30]:
                print(f"{n}: {line}")
PY

set -eu
printf '%s\n' '--- helper and vacuum references ---'
rg -n -F --glob '!*.ipynb_checkpoints/**' -- 'create_defect_point_interstitial' . || test "$?" -eq 1
rg -n -F --glob '!*.ipynb_checkpoints/**' -- 'remove_vacuum' . || test "$?" -eq 1
printf '%s\n' '--- notebook imports and relevant cells ---'
python3 - <<'PY'
import json
from pathlib import Path
p = Path('other/materials_designer/specific_examples/defect_point_adatom_island_titanium_nitride.ipynb')
d = json.loads(p.read_text())
for i, cell in enumerate(d.get('cells', [])):
    text = ''.join(cell.get('source', []))
    if any(k in text for k in ('create_defect_point_interstitial', 'remove_vacuum', 'site_spacing', 'to_json', 'VACUUM')):
        print(f'CELL {i} [{cell.get("cell_type")}]')
        print(text)
PY
printf '%s\n' '--- changed-file diff summary against supplied merge base ---'
git diff --stat 9ac071967d0ec8e38a38883ab406bfd383a48818 9e48ddf8ea1f410e277583f856d99ebe366e0347 -- other/materials_designer/specific_examples/defect_point_adatom_island_titanium_nitride.ipynb

set -eu
python3 - <<'PY'
import sys
from pathlib import Path
roots = [Path(p) for p in sys.path if p]
for root in roots:
    if root.exists():
        for p in root.glob('mat3ra/made/tools/*'):
            print(p)
PY
find /usr/local/lib /usr/lib -path '*/mat3ra/made/tools/*' -type f -print 2>/dev/null | head -200

set -eu
python3 - <<'PY'
import json
from urllib.request import Request, urlopen
url = 'https://api.github.com/repos/mat3ra/made/git/trees/main?recursive=1'
req = Request(url, headers={'Accept': 'application/vnd.github+json', 'User-Agent': 'review-inspector'})
with urlopen(req, timeout=20) as r:
    data = json.load(r)
for item in data.get('tree', []):
    if item.get('type') == 'blob' and item.get('path', '').endswith(('.py', '.pyi')):
        print(item['path'])
PY

set -eu
python3 - <<'PY'
from urllib.request import Request, urlopen
base = 'https://raw.githubusercontent.com/mat3ra/made/main/'
paths = [
    'src/py/mat3ra/made/tools/helpers.py',
    'src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/builder.py',
    'src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/configuration.py',
    'tests/py/unit/test_tools_build_defect/test_point_defect.py',
]
for path in paths:
    print(f'--- {path} ---')
    req = Request(base + path, headers={'User-Agent': 'review-inspector'})
    with urlopen(req, timeout=20) as r:
        text = r.read().decode()
    for n, line in enumerate(text.splitlines(), 1):
        if path.endswith('helpers.py') and not any(k in line for k in ('create_defect_point_interstitial', 'point_defect')):
            continue
        print(f'{n}: {line}')
PY

set -eu
python3 - <<'PY'
from urllib.request import Request, urlopen
base = 'https://raw.githubusercontent.com/mat3ra/made/main/'
paths = [
    'src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/interstitial/helpers.py',
    'src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/builder.py',
    'src/py/mat3ra/made/tools/build/defective_structures/zero_dimensional/point_defect/base/configuration.py',
    'src/py/mat3ra/made/tools/build_components/entities/auxiliary/zero_dimensional/point_defect_site/configuration.py',
    'src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/builder.py',
    'src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/configuration.py',
    'src/py/mat3ra/made/tools/modify.py',
]
for path in paths:
    print(f'--- {path} ---')
    req = Request(base + path, headers={'User-Agent': 'review-inspector'})
    with urlopen(req, timeout=20) as r:
        text = r.read().decode()
    for n, line in enumerate(text.splitlines(), 1):
        print(f'{n}: {line}')
PY

set -eu
python3 - <<'PY'
from urllib.request import Request, urlopen
base = 'https://raw.githubusercontent.com/mat3ra/made/main/'
paths = [
    'src/py/mat3ra/made/tools/operations/core/binary.py',
    'src/py/mat3ra/made/material.py',
    'src/py/mat3ra/made/basis/coordinates.py',
]
for path in paths:
    print(f'--- {path} ---')
    req = Request(base + path, headers={'User-Agent': 'review-inspector'})
    with urlopen(req, timeout=20) as r:
        text = r.read().decode()
    for n, line in enumerate(text.splitlines(), 1):
        if path.endswith('binary.py') or 'add_atoms_from_another_basis' in line or 'def add_atoms' in line:
            print(f'{n}: {line}')
PY

set -eu
python3 - <<'PY'
from urllib.request import Request, urlopen
path = 'src/py/mat3ra/made/tools/operations/core/utils.py'
url = 'https://raw.githubusercontent.com/mat3ra/made/main/' + path
req = Request(url, headers={'User-Agent': 'review-inspector'})
with urlopen(req, timeout=20) as r:
    text = r.read().decode()
for n, line in enumerate(text.splitlines(), 1):
    print(f'{n}: {line}')
PY