run fap-after-opus-1
transcript /Users/yue/.claude/projects/-Users-yue-rietx-agent-runs-2026-10-01-wp1504-figure-work-fap-after-opus-1/a34ecfaa-942f-4510-8287-d50777d94277.jsonl

   #  offset    dur    chars     tool       head
   1     3.4    2.5     4283     Bash       ls; cat fluorapatite.cif; P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/a
   2     8.7    4.4      503     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "
   3    15.7    0.1     1106     Bash       cd /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-
   4    18.4    0.1     9536     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-p
   5    21.0    0.1    17518     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-p
   6    25.6    3.8     7042     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "
   7    32.6    0.0   263888     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/fap-after-opus-1/probe.png
   8    44.9    0.1     5884     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-p
   9    50.3    3.8       14     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "
  10    55.9    0.0   234748     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/fap-after-opus-1/probe2.png
  11    64.7    2.6     3072     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "
  12    83.7    5.7      413     Bash       cat > make_figure.py <<'EOF'
  13    93.5    4.3      114     Bash       sed -i '' 's/size=(STRUCT_W, 2000)/size=STRUCT_W/' make_figure.py && ../../venvs/after/b
  14    99.6    0.0   238436     Read       /tmp/fap_preview.png
  15   109.0    3.3       33     Bash       sed -i '' 's/STRUCT_W = 1620 /STRUCT_W = 1540 /; s/PO\$_4\$ tetrahedron/PO$_4$ tetrahedr
  16   114.2    0.0   226432     Read       /tmp/fap_preview.png
  17   116.9    0.1       42     Bash       rm probe.png probe2.png && ls

17 tool calls (13 Bash, 4 Read), 0 errored
18 API calls, 2.1 min wall, 0.64 M cache-read, 41 k cache-write, 7 k output, mean context 38 k
models: claude-opus-5-5 ×18

0 traced interpreter starts, 11 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 25.3 s (0.0%)
    build                                 6      0.1 s [bond_tolerance, probability]
    render_structure                      5      4.2 s [size, view, view=c, up, up=[1, 1, 0], supersample]
