run calcite-before-opus-1
transcript /Users/yue/.claude/projects/-Users-yue-rietx-agent-runs-2026-10-01-wp1504-figure-work-calcite-before-opus-1/9ef6a0d6-8095-47a1-a34e-8164745fe621.jsonl

   #  offset    dur    chars     tool       head
   1     3.0    3.4     3514     Bash       ls; cat calcite.cif; P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before
   2     9.4   11.2      880     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/bin/python; $P -c "i
   3    23.5    3.2    10419     Bash       D=$(dirname $(/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/bin/pyth
   4    29.3    0.1      797     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/python3.12/site-
   5    31.9    0.1     4892     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/python3.12/site-
   6    35.9    9.3    20713     Bash       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/bin/python -c "
   7    47.2    0.0   180660     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/calcite-before-opus-1/figure.p
   8    53.4    2.1     2914     Bash       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/bin/python -c "
   9    65.1    3.0       70     Bash       cat > figure.py <<'EOF'
  10    81.7    2.6      341 ERR Bash       cat > figure.py <<'EOF'
  11    88.8    1.9      445 ERR Bash       sed -i '' 's/o_frac = np.unique(np.round(np.mod(\[o\["frac"\] for o in oxygens\], 1.0), 
  12    96.2    1.4       28     Bash       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/bin/python - <<'EOF'
  13    99.7    0.0    99144     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/calcite-before-opus-1/figure.p

13 tool calls (11 Bash, 2 Read), 2 errored
14 API calls, 1.8 min wall, 0.45 M cache-read, 37 k cache-write, 6 k output, mean context 35 k
models: claude-opus-5-5 ×14

0 traced interpreter starts, 9 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 32.0 s (0.0%)
    build                                 6      0.1 s [bond_tolerance, probability]
    render_structure                      3      3.9 s [path, polyhedra, polyhedra=False, hidden, hidden=['Ca']]
