q2mm/.gitignore at master · ericchansen/q2mm · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
# ── Q2MM runtime artifacts ──────────────────────────────────
timer.dat
root.log
psi4_generation.log
psi*.clean

# ── Generated Psi4 logs (large, regenerated by generate_qm_data.py) ──
examples/ch3f-sn2/psi4-output*.dat
examples/publication/rh-enamide/psi4_reference/

# ── External validation data (large, not redistributable) ──
# Dissertation supporting info: ~1.9 GB of Gaussian logs, MacroModel
# structures, and force fields. See validation/supporting-info/README.md
# for provenance and how to obtain.
validation/supporting-info/

# MM3 base force field (Copyright Columbia University 1990, "All rights
# reserved"). Not redistributable — download from atlas-nano/ATLAS_toolkit
# or extract from a MacroModel installation.
validation/published_ffs/mm3_base.fld

# ── Python ──────────────────────────────────────────────────
__pycache__/
*.py[cod]
*$py.class
*.so
*.egg-info/
*.egg
dist/
build/
*.manifest
*.spec
.installed.cfg
MANIFEST

# ── Virtual environments ───────────────────────────────────
.env
.venv
.venv*/
env/
venv/
ENV/

# ── Testing / coverage ────────────────────────────────────
.pytest_cache/
htmlcov/
.coverage
.coverage.*
coverage.xml
.tox/
.nox/
.hypothesis/

# ── Type checking ─────────────────────────────────────────
.mypy_cache/
.dmypy.json
.pyre/

# ── Editors / IDEs ────────────────────────────────────────
.idea/
*.swp
*.swo
*~

# ── OS files ──────────────────────────────────────────────
.DS_Store
Thumbs.db
Desktop.ini
$RECYCLE.BIN/

# ── MkDocs ────────────────────────────────────────────────
/site/

# ── Jupyter ───────────────────────────────────────────────
.ipynb_checkpoints/

# ── Lock files (dev-local) ────────────────────────────────
uv.lock

# ── Agent session artifacts ───────────────────────────────
*-handoff.md
copilot-session-*.md

# ── Local benchmark / convergence outputs ─────────────────
# Per AGENTS.md §6: developer-local benchmark outputs go to results/
# and stay out of git. Canonical benchmark artifacts that documentation
# references live in the separate ericchansen/q2mm-data repo.
/results/