run calcite-before-opus-3
transcript /Users/yue/.claude/projects/-private-tmp-claude-501--Users-yue-Code-rietx-0433c291-1037-42b9-8cb7-5377547150b7-scratchpad-1504-root-work-calcite-before-opus-3/c0a34ee0-3bf0-4709-a520-6b98d4753115.jsonl

   #  offset    dur    chars     tool       head
   1     4.3    1.5     6299     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   2     8.7    0.0     6560     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   3    12.5    1.3      527     Bash       cat calcite.cif | head -50; ../../venvs/before/bin/python -c "
   4    16.5    0.0   180660     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
   5    21.7    0.8     3361     Bash       ../../venvs/before/bin/python -c "
   6    29.8    0.8     1326 ERR Bash       cat > draw.py <<'EOF'
   7    35.2    1.2       76     Bash       sed -i '' 's/^sp = lambda i: g\["sites"\]\[g\["atoms"\]\[i\]\["site"\]\]\["species"\]/sp
   8    50.4    1.4       66     Bash       cat > draw.py <<'EOF'
   9    54.1    0.0    99140     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat

9 tool calls (7 Bash, 2 Read), 1 errored
10 API calls, 1.0 min wall, 0.23 M cache-read, 21 k cache-write, 4 k output, mean context 25 k
models: claude-opus-5-5 ×10

0 traced interpreter starts, 8 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 5.9 s (0.0%)
    build                                 5      0.0 s [bond_tolerance, probability]
    render_structure                      3      1.1 s [path, polyhedra, polyhedra=False, hidden, hidden=['Ca']]
