diff --git a/submissions/freshclone-3ff72d5/23e5e2ccf2ff4c48f157506f38763b6792a26f7d1b8e0a9d760a2268797af207.jsonl b/submissions/freshclone-3ff72d5/23e5e2ccf2ff4c48f157506f38763b6792a26f7d1b8e0a9d760a2268797af207.jsonl
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/workspace && python3 physics/case_brief.py --case DEV102","tool":"exec_command"},{"arguments_sha256":"37dafc7b07bc9436faee59d3fc68ccf155f77917b4c5166f5ba81bf44a4213e4","files":[],"index":1,"summary":"cd /workspace && python3 physics/candidates.py --case DEV102","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":2,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"b71253d55731d2f9a9773fc1133a63c13fceb73b6968f9ffd49185bfcf512d13","files":[],"index":3,"summary":"cd /workspace && python3 physics/screen.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"5abcbbf901dd220b6a298a3455e5eb3b31fdd6d7b4883b13c7eb75a432a33240","files":[],"index":4,"summary":"{\"chars\":\"\",\"session_id\":60906,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"3e22f341252843419865802d10ff9067c2e935535b8feddaa39da96b98bf133d","files":[],"index":5,"summary":"{\"chars\":\"\",\"session_id\":60906,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"3e22f341252843419865802d10ff9067c2e935535b8feddaa39da96b98bf133d","files":[],"index":6,"summary":"{\"chars\":\"\",\"session_id\":60906,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"4ba54007a0a569cb7c1f0b6364b280048c2a48b70e387bc196905d11ee6876ee","files":[],"index":7,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('input/manifest.json') as f:\n    m = json.load(f)\n# Look at the pattern data structure\ncase = m.get('cases', {}).get('DEV102', m)\nif isinstance(m, dict):\n    print('Top-level keys:', list(m.keys())[:20])\n\"","tool":"exec_command"},{"arguments_sha256":"cb45b204ddf354acd6581ec5e05e0916689fdb7645852394404ab408cfe30020","files":[],"index":8,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('input/manifest.json') as f:\n    m = json.load(f)\nprint('Type:', type(m).__name__)\nif isinstance(m, list):\n    print('Length:', len(m))\n    print('First item keys:', list(m[0].keys()) if isinstance(m[0], dict) else 'N/A')\nelif isinstance(m, dict):\n    print('Keys:', list(m.keys())[:30])\n\"","tool":"exec_command"},{"arguments_sha256":"98a950486e63541771e5e7056a539656b19b82ca863e2f2b17572b8a81319d71","files":[],"index":9,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('input/manifest.json') as f:\n    m = json.load(f)\ncase = m['cases']['DEV102']\nprint('Case keys:', list(case.keys()))\n# Look for pattern file info\nfor k, v in case.items():\n    if isinstance(v, str) and ('pattern' in k.lower() or 'data' in k.lower() or 'file' in k.lower()):\n        print(f'  {k}: {v[:200]}')\n    elif k in ('pattern_file', 'xrd', 'measurement'):\n        print(f'  {k}: {v}')\n\"","tool":"exec_command"},{"arguments_sha256":"57d3eee556ef3fa7c7e7dbe434d0d8854b5380085ea45daa3372931949c5f064","files":[],"index":10,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('input/manifest.json') as f:\n    m = json.load(f)\ncases = m['cases']\nprint('Type:', type(cases).__name__)\nif isinstance(cases, list):\n    print('Length:', len(cases))\n    for c in cases:\n        if isinstance(c, dict) and c.get('case_id') == 'DEV102':\n            print('Found DEV102 keys:', list(c.keys()))\n            break\nelif isinstance(cases, dict):\n    # try with DEV102\n    dev = cases.get('DEV102', cases)\n    print('DEV102 keys:', list(de","tool":"exec_command"},{"arguments_sha256":"fa750491431ba9937bbcec3cd2ecaafea3040f9ac2e5e469ee16b0a8cbf10c3b","files":[],"index":11,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('input/manifest.json') as f:\n    m = json.load(f)\ncase = m['cases'][0]\nprint('Pattern file:', case['pattern_file'])\nprint('Measurement keys:', list(case['measurement'].keys()))\nprint('Instrument profile:', case['instrument_profile'])\nprint('Chemistry:', case['chemistry_elements'])\nprint()\n# Material context\nctx = case.get('material_context', {})\nprint('Context keys:', list(ctx.keys()))\n\"","tool":"exec_command"},{"arguments_sha256":"d5da9603614c9326ab24ad0fa71d5bb5b39c7c118a7b0c9805ec1d205b4b20d7","files":[],"index":12,"summary":"find /workspace/input -name \"DEV102.xy\" 2>/dev/null && head -5 /workspace/input/DEV102.xy 2>/dev/null || find /workspace -name \"DEV102.xy\" 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"07f0dcf8205560587fc1eddb4f72b2ff7ca9fc492b82596889daa56537e31432","files":[],"index":13,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\n\ndata = np.loadtxt('input/DEV102.xy')\ntwotheta = data[:, 0]\nintensity = data[:, 1]\n\nprint(f'Points: {len(data)}')\nprint(f'2theta range: {twotheta.min():.3f} to {twotheta.max():.3f}')\nprint(f'Intensity range: {intensity.min():.1f} to {intensity.max():.1f}')\n\n# Find local maxima (peaks)\nfrom scipy.signal import find_peaks\npeaks, props = find_peaks(intensity, height=intensity.max()*0.01, distance=100)\nprint(f'\\nPeaks above 1% of max: {len(peaks)}')\n\n","tool":"exec_command"},{"arguments_sha256":"8553efd1228721628fcaff752468bb01d05370da0e40d36c257505560ce8b7c2","files":[],"index":14,"summary":"cd /workspace && python3 physics/refine.py --case DEV102 --candidates CIF001779 CIF005806 CIF005859 CIF005843 --run-label H1_search 2>&1","tool":"exec_command"},{"arguments_sha256":"07a9df56a35e9183adff842a9f3e3cfa4dbd2d54ac5faa92f3350dc3850b8615","files":[],"index":15,"summary":"{\"chars\":\"\",\"session_id\":93857,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"07a9df56a35e9183adff842a9f3e3cfa4dbd2d54ac5faa92f3350dc3850b8615","files":[],"index":16,"summary":"{\"chars\":\"\",\"session_id\":93857,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"07a9df56a35e9183adff842a9f3e3cfa4dbd2d54ac5faa92f3350dc3850b8615","files":[],"index":17,"summary":"{\"chars\":\"\",\"session_id\":93857,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"07a9df56a35e9183adff842a9f3e3cfa4dbd2d54ac5faa92f3350dc3850b8615","files":[],"index":18,"summary":"{\"chars\":\"\",\"session_id\":93857,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"b84c65a9eae333029c34924a76bcfb1b6984aadc34c3c6f8c96685b7bb12d5c6","files":[],"index":19,"summary":"cd /workspace && python3 physics/screen.py --case DEV102 --residual H1_search 2>&1","tool":"exec_command"},{"arguments_sha256":"676b798571d347f987c955b2f4ff4cb3ddc482df8533d9efd04f587db51a7bc3","files":[],"index":20,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('output/H1_search/result.json') as f:\n    r = json.load(f)\nprint('Result keys:', list(r.keys()))\nprint()\nif 'stages' in r:\n    for s in r['stages']:\n        print(f'Stage: {s[\\\"stage\\\"]}, Rwp: {s.get(\\\"Rwp\\\")}, GoF: {s.get(\\\"GoF\\\")}')\nprint()\nif 'phases' in r:\n    for p in r['phases']:\n        print(f'Phase: {p.get(\\\"candidate_id\\\")}, wt%: {p.get(\\\"weight_percent\\\")}')\n        if 'refined_cell' in p:\n            print(f'  Refined cell: {p[\\\"ref","tool":"exec_command"},{"arguments_sha256":"3303a5e543f4799c45ed27d126710f500fb099998fb4d79c25776e3d1070f831","files":[],"index":21,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('output/H1_search/result.json') as f:\n    r = json.load(f)\nprint(json.dumps(r, indent=2)[:5000])\n\"","tool":"exec_command"},{"arguments_sha256":"d1d83e5b4c266f0a71061e72d9973f7b87c8cacde1ded2f1e0152be9f031e494","files":[],"index":22,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('output/H1_search/result.json') as f:\n    r = json.load(f)\n\n# Get final Rietveld stage\nrietveld = r.get('rietveld', {})\nprint('=== Final Rietveld Stage ===')\nprint(f'Rwp: {rietveld.get(\\\"rwp\\\")}%')\nprint(f'Rexp: {rietveld.get(\\\"rexp\\\")}%')\nprint(f'GoF: {rietveld.get(\\\"gof\\\")}')\nprint(f'Converged: {rietveld.get(\\\"converged\\\")}')\nprint(f'Iterations: {rietveld.get(\\\"iteration_count\\\")}')\nprint()\nfor p in rietveld.get('phases', []):\n    print(f'Pha","tool":"exec_command"},{"arguments_sha256":"1b59a1af6f26c2258911f32094385ecc7d16aad04b48d5525cb0a21d519c9ba9","files":[],"index":23,"summary":"cd /workspace && python3 physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 CIF005843 --run-label H1_alt_Bi2O3 2>&1","tool":"exec_command"},{"arguments_sha256":"3a820bd850480c8a608459eba76926122aefcc0b588edad3532c0eb1d3642ffc","files":[],"index":24,"summary":"{\"chars\":\"\",\"session_id\":51469,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"3a820bd850480c8a608459eba76926122aefcc0b588edad3532c0eb1d3642ffc","files":[],"index":25,"summary":"{\"chars\":\"\",\"session_id\":51469,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"3a820bd850480c8a608459eba76926122aefcc0b588edad3532c0eb1d3642ffc","files":[],"index":26,"summary":"{\"chars\":\"\",\"session_id\":51469,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"9e3df2ec637aa4d1a4171940c9ede5a6bb997ebe38e74b51df431f47e845afce","files":[],"index":27,"summary":"cd /workspace && python3 physics/screen.py --case DEV102 --residual H1_alt_Bi2O3 2>&1","tool":"exec_command"},{"arguments_sha256":"d414f40dfe7f2aff0cc1c5062df361b13bf33421abb9ab542a24d8c051f24754","files":[],"index":28,"summary":"cd /workspace && python3 -c \"\n# Element balance check for H1_alt_Bi2O3 result\nimport json\n\nwith open('output/H1_alt_Bi2O3/result.json') as f:\n    r = json.load(f)\n\n# Phases and weight fractions\nphases = r['rietveld']['phases']\nweights = {p['phase_id']: p['weight_fraction'] for p in phases}\nprint('Weight fractions:')\nfor k, v in weights.items():\n    print(f'  {k}: {v:.2f}%')\nprint()\n\n# Calculate element ratios\n# CIF001783 = Bi2O3\n# CIF005806 = GeO2  \n# CIF005859 = Ge(Bi3O5)4 = GeBi12O20\n# CIF0058","tool":"exec_command"},{"arguments_sha256":"d330ca53d4e60f7474ee4ed0930bb5adc6699dc99442a0e5420e144df79dde08","files":[],"index":29,"summary":"cd /workspace && python3 physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 --run-label H1_no_GeBi2O5 2>&1","tool":"exec_command"},{"arguments_sha256":"52a6a8c796a83a1fff9e1cac97077513ff2dc3766d7a8ff0f6fac636773f1e45","files":[],"index":30,"summary":"{\"chars\":\"\",\"session_id\":89792,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"52a6a8c796a83a1fff9e1cac97077513ff2dc3766d7a8ff0f6fac636773f1e45","files":[],"index":31,"summary":"{\"chars\":\"\",\"session_id\":89792,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"e4442437beda3f305c78416510d15dbcf4705f3804bfabc198e8c6e4f35953a4","files":[],"index":32,"summary":"cd /workspace && python3 physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 CIF005844 --run-label H1_alt_GeBi2O5 2>&1","tool":"exec_command"},{"arguments_sha256":"867b134fc0ea4a95ae5f631131f9dec3c92284236a9b82762ec54ec1a31b0eed","files":[],"index":33,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"867b134fc0ea4a95ae5f631131f9dec3c92284236a9b82762ec54ec1a31b0eed","files":[],"index":34,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"867b134fc0ea4a95ae5f631131f9dec3c92284236a9b82762ec54ec1a31b0eed","files":[],"index":35,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"7e67cbf54d2d3418d64904ed95d9bb50bb0a7580423550863247293740603ac7","files":[],"index":36,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"867b134fc0ea4a95ae5f631131f9dec3c92284236a9b82762ec54ec1a31b0eed","files":[],"index":37,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"7e67cbf54d2d3418d64904ed95d9bb50bb0a7580423550863247293740603ac7","files":[],"index":38,"summary":"{\"chars\":\"\",\"session_id\":45638,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"9d5b1597f1a2e69d9e04dea17420af7e0a97d501a7dfdfd1d575656b5a86e4af","files":[],"index":39,"summary":"cd /workspace && mkdir -p output && python3 -c \"\nimport json\n\nanalysis = {\n    'case_id': 'DEV102',\n    'phases': [\n        {\n            'candidate_id': 'CIF001783',\n            'formula': 'Bi2O3',\n            'evidence': 'Ranked 2nd in screening (fom 0.60). Refined with cell shifts < 0.2%. Present as unreacted precursor.'\n        },\n        {\n            'candidate_id': 'CIF005806',\n            'formula': 'GeO2',\n            'evidence': 'Ranked 6th in screening (fom 0.32). Refined with cell sh","tool":"exec_command"},{"arguments_sha256":"cac38635feac34e31f5efc17d25179b120fcc418d7369eb188fbbbee838f436e","files":[],"index":40,"summary":"cd /workspace && python3 -c \"\nimport csv\nimport numpy as np\n\n# Read the final Rietveld curve\nwith open('output/H1_alt_Bi2O3/rietveld.csv') as f:\n    reader = csv.reader(f)\n    data = np.array(list(reader), dtype=float)\n\ntwotheta = data[:, 0]\nobserved = data[:, 1]\ncalculated = data[:, 2]\ndifference = data[:, 3]\n\n# Find peaks in the difference curve (positive = unexplained observed)\nfrom scipy.signal import find_peaks\n\n# Positive residuals (observed > calculated)\npos_peaks, pos_props = find_peaks(","tool":"exec_command"},{"arguments_sha256":"b945489124b1c37aaa191235a2bc19160d813afad08fd314e623fec78afacbf0","files":[],"index":41,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\n\n# Read the final Rietveld curve (skip header)\ndata = np.loadtxt('output/H1_alt_Bi2O3/rietveld.csv', skiprows=1)\ntwotheta = data[:, 0]\nobserved = data[:, 1]\ncalculated = data[:, 2]\ndifference = data[:, 3]\n\nfrom scipy.signal import find_peaks\n\n# Positive residuals (observed > calculated)\npos_peaks, _ = find_peaks(difference, height=50, distance=100)\npos_peaks_data = [(twotheta[p], difference[p], observed[p]) for p in pos_peaks]\npos_peaks_data.sort(","tool":"exec_command"},{"arguments_sha256":"bd0ee1b7f4bb20df9ea0bd8cfe4cededaa5dc1541f9ab803a2e4644f357d73eb","files":[],"index":42,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\n\n# Read the final Rietveld curve (skip header, comma-separated)\ndata = np.loadtxt('output/H1_alt_Bi2O3/rietveld.csv', skiprows=1, delimiter=',')\ntwotheta = data[:, 0]\nobserved = data[:, 1]\ncalculated = data[:, 2]\ndifference = data[:, 3]\n\nfrom scipy.signal import find_peaks\n\n# Positive residuals (observed > calculated)\npos_peaks, _ = find_peaks(difference, height=50, distance=100)\npos_peaks_data = [(twotheta[p], difference[p], observed[p]) for p in","tool":"exec_command"},{"arguments_sha256":"c7af4ec13945426f13e2410bc86b256c1768ac39b935b18671d0698d1f19afd9","files":[],"index":43,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\n\n# Load pattern\ndata = np.loadtxt('input/DEV102.xy')\ntwotheta = data[:, 0]\nintensity = data[:, 1]\n\n# Check peaks at unexplained positions\npeaks_of_interest = [10.38, 10.96, 11.54, 17.76, 21.73, 49.74, 52.65, 54.47, 62.27, 65.14, 71.68, 80.46, 84.48]\nmax_I = intensity.max()\nprint('Unexplained peak intensities:')\nfor p in peaks_of_interest:\n    idx = np.argmin(np.abs(twotheta - p))\n    print(f'  {p:.2f} deg: observed I={intensity[idx]:.0f} ({100*int","tool":"exec_command"},{"arguments_sha256":"8c0cd63802cd8d87c9af5bbd3e6dfbf2b48cc81dafc13e8419a5a9ead886745c","files":[],"index":44,"summary":"cd /workspace && python3 physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 CIF005843 CIF005833 --run-label H1_plus_Ge3BiO34 2>&1","tool":"exec_command"},{"arguments_sha256":"c3cdad1f8803aa99cce6279e8b0b8d5d49afb6daf522e42a37e1d6fd4c454549","files":[],"index":45,"summary":"ls /workspace/output/","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":46,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"8932a3118f5680349aa4c296a062915f6ba04c53c765d8d1cad5252b9217c386","files":[],"index":47,"summary":"cat /workspace/output/H1_plus_Ge3BiO34/result.json 2>/dev/null || echo \"NO RESULT YET\"","tool":"exec_command"},{"arguments_sha256":"6c9d5a77a33d3a63be9249686c382f2b35eca685e981e6d2e75bf5de29e55a1f","files":[],"index":48,"summary":"ls -la /workspace/output/H1_plus_Ge3BiO34/ 2>/dev/null; echo \"---\"; cat /workspace/output/analysis.json 2>/dev/null || echo \"NO ANALYSIS.YET\"","tool":"exec_command"},{"arguments_sha256":"225492f6e82d2fe192b9ad341b79a335963a7cf8c924676d14234ece8b5e8e22","files":[],"index":49,"summary":"cat /workspace/output/H1_plus_Ge3BiO34/request.json","tool":"exec_command"},{"arguments_sha256":"43f8fb0c4460b8912bab813aec37a7e4155750af0252ba45ff24feda06303e63","files":[],"index":50,"summary":"ls -la /workspace/output/H1_plus_Ge3BiO34/fit/ && cat /workspace/output/H1_plus_Ge3BiO34/fit/*.log 2>/dev/null || echo \"No log files\"","tool":"exec_command"},{"arguments_sha256":"44801ab7787506b860e1df425b64d0dc9d8e31e995e4db8a5e619ef0c33e7e75","files":[],"index":51,"summary":"cat /workspace/output/H1_alt_Bi2O3/result.json","tool":"exec_command"},{"arguments_sha256":"9ab6c80ba2803654f122316ee6da95e94399b9992138cd18c851707d18f37b74","files":[],"index":52,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H1_alt_Bi2O3 2>&1","tool":"exec_command"},{"arguments_sha256":"02d2a3c6abbf2d8337e29c96152a28349120efd6844d06bfb882acd0c657381e","files":[],"index":53,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 CIF005843 CIF005833 --run-label H2_fivephase 2>&1","tool":"exec_command"},{"arguments_sha256":"b2fac31d6b931fb6fb152c9d6de01b72db30060c90b219bddda3e468c7766059","files":[],"index":54,"summary":"{\"chars\":\"\",\"session_id\":56417,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"b2fac31d6b931fb6fb152c9d6de01b72db30060c90b219bddda3e468c7766059","files":[],"index":55,"summary":"{\"chars\":\"\",\"session_id\":56417,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"b2fac31d6b931fb6fb152c9d6de01b72db30060c90b219bddda3e468c7766059","files":[],"index":56,"summary":"{\"chars\":\"\",\"session_id\":56417,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"b2fac31d6b931fb6fb152c9d6de01b72db30060c90b219bddda3e468c7766059","files":[],"index":57,"summary":"{\"chars\":\"\",\"session_id\":56417,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"9dd24235a2fcc584919d6ae0ae4ec979520376b0e566c649b3962c589a5f1a23","files":[],"index":58,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF001783 CIF005806 CIF005859 CIF005843 CIF001780 --run-label H3_Pn3m 2>&1","tool":"exec_command"},{"arguments_sha256":"496eaeeb0007808da3260624e8947fa7b6136700fadebdba7e11e7c7a1c9d852","files":[],"index":59,"summary":"{\"chars\":\"\",\"session_id\":40523,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"496eaeeb0007808da3260624e8947fa7b6136700fadebdba7e11e7c7a1c9d852","files":[],"index":60,"summary":"{\"chars\":\"\",\"session_id\":40523,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"496eaeeb0007808da3260624e8947fa7b6136700fadebdba7e11e7c7a1c9d852","files":[],"index":61,"summary":"{\"chars\":\"\",\"session_id\":40523,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"77b5c1f4e45fca955b60f1a6c81f37c95dd37fecb636a8a0296b56fa11820cdc","files":[],"index":62,"summary":"python3 /workspace/physics/case_brief.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"d3505ed3afbef1397bbcde8d693079513a4dfac23a8272638974c586dd324216","files":[],"index":63,"summary":"python3 /workspace/physics/candidates.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"80f8c44025242fbb2af16be8b980a52a25d1b848b49b65f7a5c219ae3f7f6dcf","files":[],"index":64,"summary":"head -5 /workspace/output/H1_alt_Bi2O3/rietveld.csv && echo \"...\" && python3 -c \"\nimport csv\nwith open('/workspace/output/H1_alt_Bi2O3/rietveld.csv') as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    data = list(reader)\n\n# Find peaks in difference column\ndiff_col = header.index('difference')\ntheta_col = header.index('two_theta')\nmax_diff = max(float(r[diff_col]) for r in data)\nmin_diff = min(float(r[diff_col]) for r in data)\nmax_obs = max(float(r[header.index('observed')]) for r in ","tool":"exec_command"},{"arguments_sha256":"4cd7c3be36d80668bc6f27e45c4d3e0e736cac94155591654ffff30e264686c5","files":[],"index":65,"summary":"python3 -c \"\nimport json\nfor label in ['H1_alt_Bi2O3', 'H2_fivephase', 'H3_Pn3m']:\n    with open(f'/workspace/output/{label}/result.json') as f:\n        d = json.load(f)\n    rwp = d['rietveld']['rwp']\n    gof = d['rietveld']['gof']\n    phases = [(p['phase_id'], p['weight_fraction']) for p in d['rietveld']['phases']]\n    print(f'{label}: Rwp={rwp}%, GoF={gof:.4f}')\n    for pid, wf in phases:\n        print(f'  {pid}: {wf:.2f} wt%')\n    print()\n\"","tool":"exec_command"},{"arguments_sha256":"5c4175876b1c948d24ff917777ed6f0a9806e25817dccfb97d201f4c31903675","files":[],"index":66,"summary":"python3 -c \"\n# Element balance check from refined weight fractions\n# Phases and their stoichiometry:\n# CIF001783: Bi2O3, MM=466.1 g/mol\n# CIF005806: GeO2, MM=104.64 g/mol\n# CIF005859: Bi12GeO20, MM=2899.39 g/mol (formula sum Bi12 Ge O20)\n# CIF005843: Bi2GeO5, MM=450.1 g/mol\n\nwt = {\n    'CIF001783': 18.924382504400953,  # Bi2O3\n    'CIF005806': 31.608898474649187,  # GeO2\n    'CIF005859': 36.98689201553344,   # Bi12GeO20\n    'CIF005843': 12.479827005416414,  # Bi2GeO5\n}\n\n# Per 100g total\nmol = {}","tool":"exec_command"},{"arguments_sha256":"b9ec662cb0a78ed1904bbd3236c5c7d5dd53ffb55309ae0ed8a03d207d2fdfb2","files":[],"index":67,"summary":"cat > /workspace/output/analysis.json << 'ENDOFJSON'\n{\n  \"case_id\": \"DEV102\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF001783\",\n      \"formula\": \"Bi2O3\",\n      \"evidence\": \"Monoclinic beta-Bi2O3 (P2_1/c, No.14). Ranked 2nd in screening (fom 0.60). Refined with small cell shifts (0.10-0.15%). Present as unreacted precursor. Preferred over CIF001779 (same space group, different cell) which gave higher Rwp (6.33 vs 6.04 pct).\"\n    },\n    {\n      \"candidate_id\": \"CIF005806\",\n      \"formula\": \"G","tool":"exec_command"},{"arguments_sha256":"192a93197adc56fede9ce7b54b7b3d5a5ffbeb118c05eac2620deebfdb9773c7","files":[],"index":68,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\nprint('Valid JSON')\nprint(f'case_id: {d[\\\"case_id\\\"]}')\nprint(f'phases: {len(d[\\\"phases\\\"])}')\nfor p in d['phases']:\n    print(f'  {p[\\\"candidate_id\\\"]} {p[\\\"formula\\\"]}')\nprint(f'weight_fractions: {d[\\\"weight_fractions\\\"]}')\nprint(f'sum: {sum(d[\\\"weight_fractions\\\"].values()):.4f}')\nprint(f'fit_statistics keys: {list(d[\\\"fit_statistics\\\"].keys())}')\nprint(f'limitations: {len(d[\\\"limitations\\\"])} ite","tool":"exec_command"},{"arguments_sha256":"cbd3f11f77a007d1982abc1800c386fdf0b7bb14882f83deb8679e8e07859031","files":[],"index":69,"summary":"echo \"=== Output directory ===\" && ls -la /workspace/output/ && echo \"\" && echo \"=== CSV curve files for best fit ===\" && ls -la /workspace/output/H1_alt_Bi2O3/*.csv && echo \"\" && echo \"=== Alternative 5-phase results ===\" && ls -la /workspace/output/H2_fivephase/result.json /workspace/output/H3_Pn3m/result.json && echo \"\" && echo \"=== analysis.json size ===\" && wc -c /workspace/output/analysis.json","tool":"exec_command"}],"wall_seconds":2133.448075},"status":"completed"},"parent":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","rationale":"","root":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"43c28591f5dcf8cb67010b2f5fc42a18c0458119d0d33d93f50688112dd72dc5","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"065e32e4f29f4e6841a3f3d7186c73a43f2c5eff820cc123adba9e9c7f7f75b9","size_bytes":834183,"stage":"rietveld"},"gof":1.8875,"phases":[{"candidate_id":"CIF001783","cell":{"a":5.850499999999999,"alpha":90.0,"b":8.16934,"beta":112.981,"c":7.51277,"gamma":90.0},"spacegroup_no":14,"weight_percent":18.924382504400953,"weight_percent_error":0.18},{"candidate_id":"CIF005806","cell":{"a":4.9861699999999995,"alpha":90.0,"b":4.9861699999999995,"beta":90.0,"c":5.6466400000000005,"gamma":90.0},"spacegroup_no":152,"weight_percent":31.608898474649187,"weight_percent_error":0.22},{"candidate_id":"CIF005859","cell":{"a":10.1586,"alpha":90.0,"b":10.1586,"beta":90.0,"c":10.1586,"gamma":90.0},"spacegroup_no":197,"weight_percent":36.98689201553344,"weight_percent_error":0.18},{"candidate_id":"CIF005843","cell":{"a":15.6937,"alpha":90.0,"b":5.5056899999999995,"beta":90.0,"c":5.39176,"gamma":90.0},"spacegroup_no":36,"weight_percent":12.479827005416414,"weight_percent_error":0.16}],"quantification":"quantitative","rwp_percent":6.04,"stage":"rietveld"},"fit_basis":"43c28591f5dcf8cb67010b2f5fc42a18c0458119d0d33d93f50688112dd72dc5","fit_origin":"imported","material_sha256":"a8bad9935d65636576c8ae464a0d0118f23f7bfac9b6714e85dec656c6fd1966","measurement_sha256":"0f20379631b26f6f0e199c1c4f7214021eae920447deaba557cce6260bb1727d","phases":["CIF001783","CIF005806","CIF005859","CIF005843"]},"material":{"declared_target":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome 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"b":10.1586,"beta":90.0,"c":10.1586,"gamma":90.0},"spacegroup_no":197,"weight_percent":36.988627500361794,"weight_percent_error":0.18},{"candidate_id":"CIF005806","cell":{"a":4.9861699999999995,"alpha":90.0,"b":4.9861699999999995,"beta":90.0,"c":5.6466400000000005,"gamma":90.0},"spacegroup_no":152,"weight_percent":31.604215962847203,"weight_percent_error":0.22},{"candidate_id":"CIF001783","cell":{"a":5.850499999999999,"alpha":90.0,"b":8.16934,"beta":112.981,"c":7.51277,"gamma":90.0},"spacegroup_no":14,"weight_percent":18.932458516030696,"weight_percent_error":0.18},{"candidate_id":"CIF005843","cell":{"a":15.6936,"alpha":90.0,"b":5.50568,"beta":90.0,"c":5.39177,"gamma":90.0},"spacegroup_no":36,"weight_percent":12.474698020760307,"weight_percent_error":0.16}],"quantification":"quantitative","rwp_percent":6.04,"stage":"rietveld"},"budget_wall_seconds":3440,"completeness":{"kind":"complete"},"cost_usd":null,"end":{"answer":{"measurement":null,"next_action":null,"phases":["CIF005859","CIF005806","CIF001783","CIF005843"],"reported_weight_percent":{"CIF001783":18.93,"CIF005806":31.6,"CIF005843":12.47,"CIF005859":36.99},"reported_weight_unit":"fraction","verdict":"NOT_RECORDED"},"answer_sha256":"b9f1cfb92d6d30abc3af536cda35094ca9d79b4d96486c56e75633a905c63f43","end":"submitted"},"kind":"imported_run","trajectory":[{"arguments_sha256":"bb4a9b6e0fffd742a5c2669a41e04acadb75a047e54aabacbc9754401eead139","files":[],"index":0,"summary":"python3 /workspace/physics/case_brief.py --case DEV102","tool":"exec_command"},{"arguments_sha256":"c5f6f19cda5906ee644dfce9ad220bfe3085edae99f7d13a6d0b0425082fcf1c","files":[],"index":1,"summary":"python3 /workspace/physics/candidates.py --case DEV102","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":2,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"dc4ef3087e9562ed097015ecbcf71003a5b07da26f0c04790a59d9a0b775b952","files":[],"index":3,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"660337281f8c0e9da5e4a7bd6e7c23fb81ce83f574426294b8f358c944852599","files":[],"index":4,"summary":"{\"chars\":\"\",\"session_id\":79010,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"cd744a704ddf458d7a37cdba1308a08572205ce976a89f01edd87d2cf161527d","files":[],"index":5,"summary":"{\"chars\":\"\",\"session_id\":79010,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"cd744a704ddf458d7a37cdba1308a08572205ce976a89f01edd87d2cf161527d","files":[],"index":6,"summary":"{\"chars\":\"\",\"session_id\":79010,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"7d88e435883ab5ca5054c2e100b775be9fb076fff1a6f005465b4ca0b4c9b819","files":[],"index":7,"summary":"ls /workspace/input/","tool":"exec_command"},{"arguments_sha256":"3dff05cd7e355599bdffe84560c0a03f77d09535a07a08a00f60c317550213c3","files":[],"index":8,"summary":"head -30 /workspace/input/DEV102.xy && echo \"---\" && wc -l /workspace/input/DEV102.xy","tool":"exec_command"},{"arguments_sha256":"6e9576fb2c9dc7755e90f1849df18e382f6ac90edf1daa6e524edc1e7da69664","files":[],"index":9,"summary":"python3 -c \"\nimport numpy as np\ndata = np.loadtxt('/workspace/input/DEV102.xy')\nx = data[:,0]\ny = data[:,1]\n# Find peaks: local maxima above background\nbg = np.median(y)\nprint(f'Background median: {bg:.1f}')\nprint(f'Max intensity: {np.max(y):.1f} at {x[np.argmax(y)]:.2f} deg')\n# Find peaks above 2x background\nthreshold = 2 * bg\npeaks = []\nfor i in range(100, len(y)-100):\n    if y[i] > y[i-1] and y[i] > y[i+1] and y[i] > threshold:\n        # Find local max more carefully\n        if y[i] > np.max(","tool":"exec_command"},{"arguments_sha256":"cc6ecbc80c096af10720331dcf029c56c1dab283258f23ad1604149222d5f9fa","files":[],"index":10,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005859 CIF005806 CIF001779 CIF005843 --run-label H1_phase_search 2>&1","tool":"exec_command"},{"arguments_sha256":"aaa570ce700099cc9a84d281649ef5d5616138fbaf5e053e7118ccfc60ff2001","files":[],"index":11,"summary":"{\"chars\":\"\",\"session_id\":74865,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"aaa570ce700099cc9a84d281649ef5d5616138fbaf5e053e7118ccfc60ff2001","files":[],"index":12,"summary":"{\"chars\":\"\",\"session_id\":74865,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"aaa570ce700099cc9a84d281649ef5d5616138fbaf5e053e7118ccfc60ff2001","files":[],"index":13,"summary":"{\"chars\":\"\",\"session_id\":74865,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"aaa570ce700099cc9a84d281649ef5d5616138fbaf5e053e7118ccfc60ff2001","files":[],"index":14,"summary":"{\"chars\":\"\",\"session_id\":74865,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"fd469f315ee173e02888079fe2de57390a655da63980a16c91a028cdfd558aaa","files":[],"index":15,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV102 --residual H1_phase_search 2>&1","tool":"exec_command"},{"arguments_sha256":"e5f86c35361f9430d3f109f7eaa89f969e1c8f150817ead2f8ffce070cf979df","files":[],"index":16,"summary":"cat /workspace/output/H1_phase_search/result.json","tool":"exec_command"},{"arguments_sha256":"a0664f8d84464935e32a5e6abe075710b3ffce6a4228b010b44225e60a88d28c","files":[],"index":17,"summary":"python3 -c \"\n# Check element balance from refined weight fractions\n# MWs: Bi4GeO8 = 4*208.98 + 72.63 + 8*16.00 = 1071.55\n#      GeO2   = 72.63 + 2*16.00 = 104.63\n#      Bi2O3  = 2*208.98 + 3*16.00 = 465.96\n#      GeBi2O5 = 72.63 + 2*208.98 + 5*16.00 = 516.59\n\nmw = {'CIF005859': 1071.55, 'CIF005806': 104.63, 'CIF001779': 465.96, 'CIF005843': 516.59}\nbi_per = {'CIF005859': 4, 'CIF005806': 0, 'CIF001779': 2, 'CIF005843': 2}\nge_per = {'CIF005859': 1, 'CIF005806': 1, 'CIF001779': 0, 'CIF005843': 1}\nw","tool":"exec_command"},{"arguments_sha256":"1ac17a128dd4360e316a90e2a92ebdb0497e062a105ff292381e6929c2330245","files":[],"index":18,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005859 CIF005806 CIF001783 CIF005843 --run-label H2_1783_for_1779 2>&1","tool":"exec_command"},{"arguments_sha256":"cc84d40f9e50276deeccc34b1934720cd78541a667abcba6e09c15221621194a","files":[],"index":19,"summary":"{\"chars\":\"\",\"session_id\":47493,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"cc84d40f9e50276deeccc34b1934720cd78541a667abcba6e09c15221621194a","files":[],"index":20,"summary":"{\"chars\":\"\",\"session_id\":47493,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"cc84d40f9e50276deeccc34b1934720cd78541a667abcba6e09c15221621194a","files":[],"index":21,"summary":"{\"chars\":\"\",\"session_id\":47493,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"2a6c7b27cb87f27e844e7c4a703a06b4772ddfab7025ded61a40b0b8b0ad4b61","files":[],"index":22,"summary":"ls /workspace/input/candidates/DEV102/","tool":"exec_command"},{"arguments_sha256":"1a615faedb33e337886278d38e86278081561876d153de0169ee7adf9b3a0e39","files":[],"index":23,"summary":"grep -E \"_chemical_formula|_cell_length|_sym_space_group\" /workspace/input/candidates/DEV102/CIF005859.cif | head -10","tool":"exec_command"},{"arguments_sha256":"abee57b24210d95690d236d61825fb36b64baaba00b2c2965b81783cef04163f","files":[],"index":24,"summary":"for f in CIF005859 CIF005806 CIF001783 CIF005843; do echo \"=== $f ===\"; grep \"_chemical_formula\" /workspace/input/candidates/DEV102/${f}.cif; done","tool":"exec_command"},{"arguments_sha256":"f5524e6ca803079c203013707708fb8f4c587f9ba907cc6fa949d6059dca13ed","files":[],"index":25,"summary":"python3 -c \"\n# Element balance from H2 refined weight fractions\n# CIF formulas verified from .cif files\n# CIF005859: Bi12 Ge O20\n# CIF005806: Ge O2 (MW 104.59)\n# CIF001783: Bi2 O3\n# CIF005843: Bi2 Ge O5\n\n# Precise MWs (using standard atomic weights)\nBi = 208.98040\nGe = 72.630\nO  = 15.9994\n\nmw = {\n    'CIF005859': 12*Bi + Ge + 20*O,  # Bi12GeO20\n    'CIF005806': 104.59,              # GeO2 (from CIF)\n    'CIF001783': 2*Bi + 3*O,          # Bi2O3\n    'CIF005843': 2*Bi + Ge + 5*O,    # Bi2GeO5\n}\n\nb","tool":"exec_command"},{"arguments_sha256":"43ff6dcec03e3303e215c2a04ce757fb01f48973c36e7baab9cbe815e4d9efcf","files":[],"index":26,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV102 --residual H2_1783_for_1779 2>&1","tool":"exec_command"},{"arguments_sha256":"0041bfe07574745fd05bf867aee96ec60a7975b0b0e54f3217a3ae2fa0a47742","files":[],"index":27,"summary":"mkdir -p /workspace/output && python3 -c \"\nimport json\n\nanalysis = {\n    'case_id': 'DEV102',\n    'phases': [\n        {\n            'candidate_id': 'CIF005859',\n            'formula': 'Bi12GeO20',\n            'evidence': 'Top-ranked in screening (fom 0.50, cov 0.77, expl 41%). Identified by phase search. Rietveld refinement cell shift +0.13%. Refined wt% 36.99(18). Major phase accounting for strongest diffraction peaks.'\n        },\n        {\n            'candidate_id': 'CIF005806',\n            '","tool":"exec_command"},{"arguments_sha256":"368def902eb1ce5beed034a0f57091105c0dc9a553ba1c513add5bde87be2043","files":[],"index":28,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005859 CIF005806 CIF001783 CIF005843 CIF005833 --run-label H3_plus_5833 2>&1","tool":"exec_command"},{"arguments_sha256":"417c8429d364111dcd557d13a05b0137610a603072e3723c830ae56e6da15a08","files":[],"index":29,"summary":"{\"chars\":\"\",\"session_id\":5992,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"417c8429d364111dcd557d13a05b0137610a603072e3723c830ae56e6da15a08","files":[],"index":30,"summary":"{\"chars\":\"\",\"session_id\":5992,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"417c8429d364111dcd557d13a05b0137610a603072e3723c830ae56e6da15a08","files":[],"index":31,"summary":"{\"chars\":\"\",\"session_id\":5992,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"417c8429d364111dcd557d13a05b0137610a603072e3723c830ae56e6da15a08","files":[],"index":32,"summary":"{\"chars\":\"\",\"session_id\":5992,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"cd6009d314d1a66463c0547682de5a34bc3885c6c2292d12c8d49a0959b868df","files":[],"index":33,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV102 --residual H3_plus_5833 2>&1","tool":"exec_command"},{"arguments_sha256":"da54064eb80f8f8bc2d9016b150bd0ca83d3d9ae4d1d518b8ddcae3b8cce20f0","files":[],"index":34,"summary":"python3 -c \"\nimport json\n\nanalysis = {\n    'case_id': 'DEV102',\n    'phases': [\n        {\n            'candidate_id': 'CIF005859',\n            'formula': 'Bi12GeO20',\n            'evidence': 'Top-ranked non-precursor in screening (fom 0.50, cov 0.77, expl 41%). Identified by phase search as dominant product (38.3% in search fit). Rietveld refinement: wt% 36.99(18), cell shift +0.13%, converged. Largest single contributor to observed pattern; accounts for strongest peak at 28.07 deg and other maj","tool":"exec_command"},{"arguments_sha256":"4c845dee39de5bf83c727c19d07a5583e308c77bfdf842cca9c0265ea477e9a8","files":[],"index":35,"summary":"ls -la /workspace/output/ && echo \"---\" && ls -la /workspace/output/H2_1783_for_1783/ 2>/dev/null || ls -la /workspace/output/H2_1783_for_1779/ 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"68790b602e965bba7abcc1c6a5fb2baf8c23604852bca2f0b7cb33fcdc9bf51a","files":[],"index":36,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":37,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"fbb4ced7712e81ac7be4418cc897ad50d1ae12b9a30f31706847097a5584dad7","files":[],"index":38,"summary":"cat /workspace/output/H2_1783_for_1779/result.json | python3 -m json.tool | head -120","tool":"exec_command"},{"arguments_sha256":"02b9ce042b2314ef89a63f1ebcf827b3025a6a882e394ecf1c19d0971204c11b","files":[],"index":39,"summary":"cat /workspace/output/H2_1783_for_1779/result.json | python3 -m json.tool | tail -200","tool":"exec_command"},{"arguments_sha256":"56650e1a242baac2b61085fce637b52026009ef628b8056fbfa5ebfe7181bd13","files":[],"index":40,"summary":"cat /workspace/output/H3_plus_5833/result.json | python3 -m json.tool | grep -A5 \"weight_fraction\"","tool":"exec_command"},{"arguments_sha256":"77b5c1f4e45fca955b60f1a6c81f37c95dd37fecb636a8a0296b56fa11820cdc","files":[],"index":41,"summary":"python3 /workspace/physics/case_brief.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"d3505ed3afbef1397bbcde8d693079513a4dfac23a8272638974c586dd324216","files":[],"index":42,"summary":"python3 /workspace/physics/candidates.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"df1a3acfbde40e22fa9c9227b6f721fefbdab182343461dd4a69b52e30a3c612","files":[],"index":43,"summary":"python3 /workspace/physics/screen.py --residual H2_1783_for_1779 2>&1","tool":"exec_command"},{"arguments_sha256":"e91e2e0bf966ac96940a796293cf918a8c60ae64253e6a73da71bf6d36bc4a7a","files":[],"index":44,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H2_1783_for_1779 2>&1","tool":"exec_command"},{"arguments_sha256":"7e9a045139fb61e6e5ab417436d512fa536ebbe3c2cb381616eb2dfa4893c025","files":[],"index":45,"summary":"python3 << 'PYEOF'\nimport json\n\n# Molecular weights\nBi = 208.98040\nGe = 72.63\nO = 15.9994\n\n# Phase formulas and refined weight fractions from H2 rietveld stage\nphases = {\n    \"CIF005859\": {\"formula\": \"Bi12GeO20\", \"Bi\": 12, \"Ge\": 1, \"O\": 20, \"wt\": 36.988627500361794},\n    \"CIF005806\": {\"formula\": \"GeO2\", \"Bi\": 0, \"Ge\": 1, \"O\": 2, \"wt\": 31.604215962847203},\n    \"CIF001783\": {\"formula\": \"Bi2O3\", \"Bi\": 2, \"Ge\": 0, \"O\": 3, \"wt\": 18.932458516030696},\n    \"CIF005843\": {\"formula\": \"Bi2GeO5\", \"Bi\": 2, \"G","tool":"exec_command"},{"arguments_sha256":"d8608e3dceb7cf1ef943e69710361ea0f77a4e52dd95ef2c0e4a5f556c4675db","files":[],"index":46,"summary":"head -5 /workspace/output/H2_1783_for_1779/rietveld.csv && echo \"...\" && tail -3 /workspace/output/H2_1783_for_1779/rietveld.csv","tool":"exec_command"},{"arguments_sha256":"2b52d7b5882830973be2f586c97e2b58d6c10edde7c88c00ba822fb6dff4c514","files":[],"index":47,"summary":"python3 << 'PYEOF'\nimport csv\n\n# Read the rietveld.csv and find the largest |difference| peaks\nwith open(\"/workspace/output/H2_1783_for_1779/rietveld.csv\") as f:\n    reader = csv.DictReader(f)\n    rows = list(reader)\n\n# Find max observed for percentage calculation\nmax_obs = max(float(r[\"observed\"]) for r in rows)\nprint(f\"Max observed counts: {max_obs:.0f}\")\n\n# Find top 15 positive differences (observed > calculated)\npositive = sorted(rows, key=lambda r: float(r[\"difference\"]), reverse=True)[:15]","tool":"exec_command"},{"arguments_sha256":"c9fac17375143322dcdc89c40b2fd89eb409257ce4c60bc79c8a5f4c0b098a00","files":[],"index":48,"summary":"python3 << 'PYEOF'\nimport json\n\nanalysis = {\n    \"case_id\": \"DEV102\",\n    \"phases\": [\n        {\n            \"candidate_id\": \"CIF005859\",\n            \"formula\": \"Bi12GeO20 (Ge(Bi3O5)4, I23)\",\n            \"evidence\": \"Top-ranked non-precursor in screening. Dominant Rietveld component (36.99%). Cell shift +0.12% from CIF (10.1455 -> 10.1586 A). Identifies the strongest peak at ~28.0 deg. Confirmed by all three refinement runs (H1, H2, H3).\"\n        },\n        {\n            \"candidate_id\": \"CIF00580","tool":"exec_command"},{"arguments_sha256":"91c4713731ee7e03ecae68501b54217ae6eb4cc8f54532dc8020ee9841f4a4ea","files":[],"index":49,"summary":"python3 -c \"import json; d=json.load(open('/workspace/output/analysis.json')); print('Valid JSON'); print('Keys:', list(d.keys())); print('Phases:', len(d['phases'])); print('Weight fractions sum:', sum(d['weight_fractions'].values())); print('ESD fields check:'); [print(f'  {k}: {type(v).__name__}') for k,v in d.get('fit_statistics',{}).items() if 'esd' in k.lower() or 'error' in k.lower()]\"","tool":"exec_command"},{"arguments_sha256":"793ab1abefbf09cb0c327072e57f4d098f5490ac11e847cc2b1e50dc2510d3ae","files":[],"index":50,"summary":"python3 -c \"\nimport json\nr = json.load(open('/workspace/output/H1_phase_search/result.json'))\n# Get the rietveld stage\nrietveld = r['rietveld']\nprint('H1 Rietveld final stage:')\nprint(f'  Rwp: {rietveld[\\\"rwp\\\"]}%')\nprint(f'  Rp: {rietveld[\\\"rp\\\"]}%')\nprint(f'  GoF: {rietveld[\\\"gof\\\"]}')\nprint(f'  Converged: {rietveld[\\\"converged\\\"]}')\nfor p in rietveld['phases']:\n    print(f'  {p[\\\"phase_id\\\"]}: {p[\\\"weight_fraction\\\"]:.2f}%')\nprint()\nprint('Stage degradation:')\nfor k,v in r.get('stage_degradat","tool":"exec_command"},{"arguments_sha256":"9d42c6e29e5e848aaac09adaf9796a5760ee304d2f37b1ce628e20fa98ff19b0","files":[],"index":51,"summary":"cat /workspace/output/analysis.json | python3 -m json.tool","tool":"exec_command"},{"arguments_sha256":"f1064997cb87d6f68117fad0927c84abb111551af72272e7e4c13308f826e573","files":[],"index":52,"summary":"find /workspace/output -type f | sort","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":53,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"c11a466cbdd11094d72b1f9b89170e28770f106ac0b0c48c92c68ee00da8040f","files":[],"index":54,"summary":"ls -la /workspace/output/","tool":"exec_command"},{"arguments_sha256":"7b84ea55cb1597b82373050ee00591a02dabdb0563466701f8abdea3ff44d9e3","files":[],"index":55,"summary":"ls -la /workspace/output/H2_1783_for_1779/ 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"68790b602e965bba7abcc1c6a5fb2baf8c23604852bca2f0b7cb33fcdc9bf51a","files":[],"index":56,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"5835d3f1accf17fb2375c13ba9e542e2f951a099dbaaa9bc0ba5fd172f07e800","files":[],"index":57,"summary":"cat /workspace/output/H2_1783_for_1779/result.json","tool":"exec_command"},{"arguments_sha256":"7354c5ccc9846d5beeef65cd1603bd99027874b6c7fefffc0ee8f9cc1bf67997","files":[],"index":58,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H3_plus_5833/result.json') as f:\n    r = json.load(f)\nstage = r.get('rietveld', {})\nprint('H3 Rietveld stage:')\nprint(f'  Rwp: {stage.get(\\\"rwp\\\")}')\nprint(f'  GoF: {stage.get(\\\"gof\\\")}')\nprint(f'  Durbin-Watson: {stage.get(\\\"durbin_watson\\\")}')\nprint(f'  Converged: {stage.get(\\\"converged\\\")}')\nprint('  Phases:')\nfor p in stage.get('phases', []):\n    print(f'    {p[\\\"phase_id\\\"]}: {p[\\\"weight_fraction\\\"]:.4f}% (error={p.get(\\\"weight_fraction_","tool":"exec_command"},{"arguments_sha256":"7dba6fdcabddaf3ebf4a36128a93a861714fb5c0d91bad9d745550d5a716555b","files":[],"index":59,"summary":"python3 -c \"\nimport json\n\n# H2 final Rietveld weight fractions\nwts = {\n    'CIF005859': 36.9886,  # Bi12GeO20  -> Bi: 12, Ge: 1\n    'CIF005806': 31.6042,  # GeO2       -> Bi: 0, Ge: 1\n    'CIF001783': 18.9325,  # Bi2O3      -> Bi: 2, Ge: 0\n    'CIF005843': 12.4747,  # Bi2GeO5    -> Bi: 2, Ge: 1\n}\n\n# Atomic masses\nM_Bi = 208.98040\nM_Ge = 72.63\nM_O  = 15.9994\n\n# Molar masses of each phase\nphase_composition = {\n    'CIF005859': {'Bi': 12, 'Ge': 1, 'O': 20},   # Bi12GeO20\n    'CIF005806': {'Bi': 0, ","tool":"exec_command"},{"arguments_sha256":"382501eb91508742e424a0853dec2878b566e81c741b3bd80e5ecb60581eb079","files":[],"index":60,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H1_phase_search/result.json') as f:\n    r = json.load(f)\nstage = r.get('rietveld', {})\nprint('H1 (CIF001779) Rietveld stage:')\nprint(f'  Rwp: {stage.get(\\\"rwp\\\")}')\nprint(f'  Rp: {stage.get(\\\"rp\\\")}')\nprint(f'  Rpb: {stage.get(\\\"rpb\\\")}')\nprint(f'  GoF: {stage.get(\\\"gof\\\")}')\nprint(f'  Durbin-Watson: {stage.get(\\\"durbin_watson\\\")}')\nprint(f'  Converged: {stage.get(\\\"converged\\\")}')\nprint(f'  Iterations: {stage.get(\\\"iteration_count\\\")}')\nprin","tool":"exec_command"},{"arguments_sha256":"8cd890d30c1f31b1322b1920a42d841de68d76261c86f6164b661917c5dc5e9e","files":[],"index":61,"summary":"python3 -c \"\nimport csv\n\n# Check the largest positive and negative residuals from H2 rietveld.csv\nmax_pos = (0, 0, 0)  # (residual, two_theta, observed)\nmax_neg = (0, 0, 0)\ncount = 0\n\nwith open('/workspace/output/H2_1783_for_1779/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    for row in reader:\n        diff = float(row['difference'])\n        t2 = float(row['two_theta'])\n        obs = float(row['observed'])\n        count += 1\n        if diff > max_pos[0]:\n            max_pos = (diff, t2,","tool":"exec_command"},{"arguments_sha256":"9bee559d1cc9a7e9ecfb96f3230033703c4e62530eab75201a068ced55cd6611","files":[],"index":62,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H2_1783_for_1779 2>&1 | head -80","tool":"exec_command"},{"arguments_sha256":"e6ee3ddf4e32d5ad5158ae252f02e94bc4ba1fd88b43c70cfdedbb4226d1d496","files":[],"index":63,"summary":"python3 /workspace/physics/screen.py --case DEV102 2>&1 | head -120","tool":"exec_command"},{"arguments_sha256":"d336da3098b3708a8eed0467f9d07f86a4e7486cc1035d71835fdc55d173c301","files":[],"index":64,"summary":"{\"chars\":\"\",\"session_id\":26263,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"7665db533c7eab3d76a9949ed9250ab9495059bb78a8252e4e074df31615d26b","files":[],"index":65,"summary":"{\"chars\":\"\",\"session_id\":26263,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"30d9c57f1a7723e491b09468fcc67d03a0822054b485d0417fdc4ef7b9ed2f1c","files":[],"index":66,"summary":"{\"chars\":\"\",\"session_id\":26263,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"0b6c9e0a6b714f826d7a5565ccd66ccaa84e54ce9e07d6b5d73fff4db5aa75da","files":[],"index":67,"summary":"python3 -c \"\n# Final verification of all key numbers from H2 result.json\nimport json\nwith open('/workspace/output/H2_1783_for_1779/result.json') as f:\n    r = json.load(f)\n\nriv = r['rietveld']\npaw = r['pawley']\n\n# Weight fractions\nwts = {}\nfor p in riv['phases']:\n    wts[p['phase_id']] = p['weight_fraction']\n    shift = {}\n    lp = p['lattice_params']\n    lpi = p['lattice_params_initial']\n    for k in lp:\n        if k in ('alpha','beta','gamma') and lp[k] == 90:\n            continue\n        if l","tool":"exec_command"},{"arguments_sha256":"f858d9f8d9e5952080b63b5758ed5f9e967b35bb61951d775072f315d4102244","files":[],"index":68,"summary":"cat > /workspace/output/analysis.json << 'ENDOFFILE'\n{\n  \"case_id\": \"DEV102\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF005859\",\n      \"formula\": \"Bi12GeO20 (Ge(Bi3O5)4, I23)\",\n      \"evidence\": \"Top-ranked non-precursor in screening (fom 0.50, rank 3 of 20). Dominant Rietveld component (36.99%). Cell shift +0.13% from CIF (a: 10.1455 -> 10.1586 A). Identifies the strongest peak at ~28.0 deg. Confirmed across all three refinement runs (H1, H2, H3).\"\n    },\n    {\n      \"candidate_id\": \"CIF005","tool":"exec_command"},{"arguments_sha256":"1535281d6e71bd6ed6c0f6d6d41eb4c2b232ce76875b1588743b735f69e15557","files":[],"index":69,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\nprint('Valid JSON')\nprint(f'File size: {len(json.dumps(d, indent=2))} chars')\nprint(f'Fields: {list(d.keys())}')\nprint(f'Phases: {len(d[\\\"phases\\\"])}')\nprint(f'Weight fractions: {d[\\\"weight_fractions\\\"]}')\nprint(f'Sum of fractions: {sum(d[\\\"weight_fractions\\\"].values()):.4f}')\nprint(f'Fit statistics: {list(d[\\\"fit_statistics\\\"].keys())}')\nprint(f'Uncertainties sections: {list(d[\\\"uncertainties\\\"].key","tool":"exec_command"},{"arguments_sha256":"ff7fca35cf8674eefec9459052fa92daa448f1092887424d1440160f81904a6d","files":[],"index":70,"summary":"python3 -c \"\nimport json, os\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\nprint('Artifact verification:')\nfor p in d['fit_artifacts']:\n    exists = os.path.exists(p)\n    size = os.path.getsize(p) if exists else 0\n    print(f'  {\\\"OK\\\" if exists else \\\"MISSING\\\"}: {p} ({size:,} bytes)')\nprint()\n# Verify the screen.py --residual output was run (it uses H2_1783_for_1779)\nimport subprocess\nprint('screen.py --residual verification:')\nresult = subprocess.run(['python3', '/wo","tool":"exec_command"},{"arguments_sha256":"e6c1024d55333e233af006c471822875c8fc289e7e0a979a1aaf3eb581e30aee","files":[],"index":71,"summary":"python3 -c \"\nimport json\n\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\n\n# Verify weight fractions sum to 1.0\nwts = d['weight_fractions']\ns = sum(wts.values())\nassert abs(s - 1.0) < 0.01, f'Fractions sum to {s}, not ~1.0'\n\n# Verify all phase IDs match weight fraction keys\nphase_ids = [p['candidate_id'] for p in d['phases']]\nwt_keys = list(wts.keys())\nassert set(phase_ids) == set(wt_keys), f'Mismatch: phases={phase_ids}, wts={wt_keys}'\n\n# Verify required fields\nrequired ","tool":"exec_command"}],"wall_seconds":1904.187478},"status":"completed"},"parent":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","rationale":"","root":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"59dabd55990c3c4590d74d37ff4ab099d87648fb4d981382cb73b184853f696a","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"e5c9d4c3606b4d6aafb502986ba7ad921db6ad2f4c1ed1030fc7f7a694b4444a","size_bytes":834183,"stage":"rietveld"},"gof":1.8875,"phases":[{"candidate_id":"CIF005859","cell":{"a":10.1586,"alpha":90.0,"b":10.1586,"beta":90.0,"c":10.1586,"gamma":90.0},"spacegroup_no":197,"weight_percent":36.988627500361794,"weight_percent_error":0.18},{"candidate_id":"CIF005806","cell":{"a":4.9861699999999995,"alpha":90.0,"b":4.9861699999999995,"beta":90.0,"c":5.6466400000000005,"gamma":90.0},"spacegroup_no":152,"weight_percent":31.604215962847203,"weight_percent_error":0.22},{"candidate_id":"CIF001783","cell":{"a":5.850499999999999,"alpha":90.0,"b":8.16934,"beta":112.981,"c":7.51277,"gamma":90.0},"spacegroup_no":14,"weight_percent":18.932458516030696,"weight_percent_error":0.18},{"candidate_id":"CIF005843","cell":{"a":15.6936,"alpha":90.0,"b":5.50568,"beta":90.0,"c":5.39177,"gamma":90.0},"spacegroup_no":36,"weight_percent":12.474698020760307,"weight_percent_error":0.16}],"quantification":"quantitative","rwp_percent":6.04,"stage":"rietveld"},"fit_basis":"59dabd55990c3c4590d74d37ff4ab099d87648fb4d981382cb73b184853f696a","fit_origin":"imported","material_sha256":"a8bad9935d65636576c8ae464a0d0118f23f7bfac9b6714e85dec656c6fd1966","measurement_sha256":"0f20379631b26f6f0e199c1c4f7214021eae920447deaba557cce6260bb1727d","phases":["CIF005859","CIF005806","CIF001783","CIF005843"]},"material":{"declared_target":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger target_compound"},"value":"Ge2Bi2O7"},"declared_target_stoichiometry":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger target_stoichiometry"},"value":"Bi2O3-2GeO2"},"elements":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"elements of the declared precursors"},"value":["Bi","Ge","O"]},"elements_basis":"declared","precursors":[{"amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_actual_masses"},"value":{"unit":"g","value":1.38156}},"cas_number":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].cas_number"},"value":"1304-76-3"},"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].formula"},"value":"Bi2O3"},"name":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].name"},"value":"bismuth(iii) oxide"},"purity":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].sa_purity"},"value":0.9990000000000001},"target_amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_target_masses"},"value":{"unit":"g","value":1.38014}}},{"amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_actual_masses"},"value":{"unit":"g","value":0.62231}},"cas_number":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].cas_number"},"value":"1310-53-8"},"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].formula"},"value":"GeO2"},"name":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].name"},"value":"germanium(iv) oxide"},"purity":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].sa_purity"},"value":0.9999800000000001},"target_amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_target_masses"},"value":{"unit":"g","value":0.61986}}}],"processing":[{"atmosphere":null,"cooling":null,"cooling_rate_c_per_min":null,"duration_min":null,"equipment":null,"furnace":null,"heating_rate_c_per_min":null,"mass_mg":null,"met_target_mass":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.met_target_mass"},"value":true},"operation":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger workflow_spec.steps[PowderDosing].action"},"value":"dose"},"order":1,"temperature_c":null,"temperature_profile":null},{"atmosphere":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger not recorded: the ledger has no atmosphere field"},"value":null},"cooling":null,"cooling_rate_c_per_min":null,"duration_min":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.heating_time"},"value":60.0},"equipment":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger 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2>&1","tool":"exec_command"},{"arguments_sha256":"94b03d8c872a03d765ccfb062ca3f0550dd6ce9525aa047a97673809e9328861","files":[],"index":4,"summary":"{\"chars\":\"\",\"session_id\":89889,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"f95c981d7be434e340342cc19e6cb4416c58c29d11051481838d102ccc92b67b","files":[],"index":5,"summary":"{\"chars\":\"\",\"session_id\":89889,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"a0fcc957f47dc5d824b2cddadbd43f43aabe2709743b21c6a2fa64b2d4bd8478","files":[],"index":6,"summary":"{\"chars\":\"\",\"session_id\":89889,\"yield_time_ms\":90000}","tool":"write_stdin"},{"arguments_sha256":"ec526d892a7f7836421a5b9c2de8a5186805c8974bfffdd7275dc66447f901ae","files":[],"index":7,"summary":"mkdir -p /workspace/output && python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001779 CIF005859 CIF005843 --run-label H1_search 2>&1","tool":"exec_command"},{"arguments_sha256":"282b553cca6ea06b03b489d0181ba94bde4a1027821e02204f9a042c618d19fd","files":[],"index":8,"summary":"{\"chars\":\"\",\"session_id\":77703,\"yield_time_ms\":90000}","tool":"write_stdin"},{"arguments_sha256":"282b553cca6ea06b03b489d0181ba94bde4a1027821e02204f9a042c618d19fd","files":[],"index":9,"summary":"{\"chars\":\"\",\"session_id\":77703,\"yield_time_ms\":90000}","tool":"write_stdin"},{"arguments_sha256":"282b553cca6ea06b03b489d0181ba94bde4a1027821e02204f9a042c618d19fd","files":[],"index":10,"summary":"{\"chars\":\"\",\"session_id\":77703,\"yield_time_ms\":90000}","tool":"write_stdin"},{"arguments_sha256":"c5bc56a3cc4d4e11ab9d8ea1d12a8670dc281113c9ff8d5a797b2fad14e3433a","files":[],"index":11,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H1_search 2>&1","tool":"exec_command"},{"arguments_sha256":"51fc6b9f4fb96a4c995b2857c479ddf95839280dee7fd469d6855b72d544470d","files":[],"index":12,"summary":"cat /workspace/output/H1_search/result.json","tool":"exec_command"},{"arguments_sha256":"d6f9e3422c67d884b593bee78a23066fbc2c1bceb67262eac3738cde2a979346","files":[],"index":13,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001783 CIF005859 CIF005843 --run-label H2_Bi2O3_v2 2>&1","tool":"exec_command"},{"arguments_sha256":"074915b708a3831e00cc38a83d47fbbe8c89918a23515fafa6ae6f3ebc260156","files":[],"index":14,"summary":"{\"chars\":\"\",\"session_id\":78440,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"074915b708a3831e00cc38a83d47fbbe8c89918a23515fafa6ae6f3ebc260156","files":[],"index":15,"summary":"{\"chars\":\"\",\"session_id\":78440,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"4907434ca4805e917bdb15e652122d76d1f5dfae2bc4f956bc1b1dc8a00f4d51","files":[],"index":16,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H2_Bi2O3_v2 2>&1","tool":"exec_command"},{"arguments_sha256":"c5bd55973776b83aefee2ec08d5ba78311ffc0c04e8ab6802fb637502b34bf03","files":[],"index":17,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001783 CIF005859 CIF005844 --run-label H3_GeBi2O5_pnma 2>&1","tool":"exec_command"},{"arguments_sha256":"1adf767deaab5c78e1981b65d88dd8ef2ee5461dff7c6d8d4fecf2174f50b26d","files":[],"index":18,"summary":"{\"chars\":\"\",\"session_id\":80854,\"yield_time_ms\":180000}","tool":"write_stdin"},{"arguments_sha256":"1adf767deaab5c78e1981b65d88dd8ef2ee5461dff7c6d8d4fecf2174f50b26d","files":[],"index":19,"summary":"{\"chars\":\"\",\"session_id\":80854,\"yield_time_ms\":180000}","tool":"write_stdin"},{"arguments_sha256":"0be80ad01b6f0e2140c07b805cbe874a815433a5bb31d450a7678d336909eeda","files":[],"index":20,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001783 CIF005859 --run-label H4_no_GeBi2O5 2>&1","tool":"exec_command"},{"arguments_sha256":"4f9c455d04d8d48e034caf6468df61f8da03e0f44f90a8b3e305e19db2b4abde","files":[],"index":21,"summary":"{\"chars\":\"\",\"session_id\":31866,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"37c9d0eb0d9879c8ffbe7f1e646ac0ab2c8450243e5d6bfdd005ada5ce7dc9e7","files":[],"index":22,"summary":"cat > /workspace/output/analysis.json << 'ANALYSIS_EOF'\n{\n  \"case_id\": \"DEV102\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF005859\",\n      \"formula\": \"Ge(Bi3O5)4\",\n      \"evidence\": \"Top-ranked ternary phase in screening (fom 0.50). Refinement cell shift +0.13%. Contributes 36.99 wt% to Rietveld fit.\"\n    },\n    {\n      \"candidate_id\": \"CIF005806\",\n      \"formula\": \"GeO2\",\n      \"evidence\": \"Pinned precursor phase, highest fom among GeO2 polymorphs (0.32). Refinement cell shifts -0.06 to -0.1","tool":"exec_command"},{"arguments_sha256":"947d26746600e404b96553ffe07453361fac57912093c960d49803f1f29cd976","files":[],"index":23,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005846 CIF001783 CIF005859 CIF005843 --run-label H5_GeO2_pbcn 2>&1","tool":"exec_command"},{"arguments_sha256":"0158ae5d3c7dd7c9ff6f89452767c09f8c6ad25e5be03d4464be9329463b97ca","files":[],"index":24,"summary":"{\"chars\":\"\",\"session_id\":13334,\"yield_time_ms\":180000}","tool":"write_stdin"},{"arguments_sha256":"0158ae5d3c7dd7c9ff6f89452767c09f8c6ad25e5be03d4464be9329463b97ca","files":[],"index":25,"summary":"{\"chars\":\"\",\"session_id\":13334,\"yield_time_ms\":180000}","tool":"write_stdin"},{"arguments_sha256":"a44500b9bee0531d5daa143790db8a09a8fce40e2973d5d26936c5a91ba3fff6","files":[],"index":26,"summary":"cat /workspace/output/H2_Bi2O3_v2/result.json | python3 -c \"import json,sys; d=json.load(sys.stdin); r=d['rietveld']; print('Final Rietveld:'); print(f'  Rwp={r[\\\"rwp\\\"]}%, Rp={r[\\\"rp\\\"]}%, Rpb={r[\\\"rpb\\\"]}%, Rexp={r[\\\"rexp\\\"]}%, GoF={r[\\\"gof\\\"]:.4f}'); print(f'  DW={r[\\\"durbin_watson\\\"]:.2f}'); print(f'  Iterations={r[\\\"iteration_count\\\"]}'); print(f'  Converged={r[\\\"converged\\\"]}'); print('Phase details:'); [print(f'  {p[\\\"phase_id\\\"]}: wf={p[\\\"weight_fraction\\\"]:.2f}%, lattice params: {p[\\\"la","tool":"exec_command"},{"arguments_sha256":"2af14decd15638b2cccf0ad59cce442ac00c6ed8865b15a96d99cb1a166bb4b7","files":[],"index":27,"summary":"python3 -c \"\nimport json,sys\nd=json.load(open('/workspace/output/H2_Bi2O3_v2/result.json'))\nr=d['rietveld']\nprint('Final Rietveld:')\nprint(f'  Rwp={r[\\\"rwp\\\"]}%, Rp={r[\\\"rp\\\"]}%, Rpb={r[\\\"rpb\\\"]}%, Rexp={r[\\\"rexp\\\"]}%, GoF={r[\\\"gof\\\"]:.4f}')\nprint(f'  DW={r[\\\"durbin_watson\\\"]:.2f}')\nprint(f'  Iterations={r[\\\"iteration_count\\\"]}')\nprint(f'  Converged={r[\\\"converged\\\"]}')\nprint('Phase details:')\nfor p in r['phases']:\n    print(f'  {p[\\\"phase_id\\\"]}: wf={p[\\\"weight_fraction\\\"]:.2f}%, params={p[\\\"la","tool":"exec_command"},{"arguments_sha256":"3aa16f76281a8b0db6069d3535d42d83f7dd35916d9da8a3d6690b999edce58a","files":[],"index":28,"summary":"python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001783 CIF005859 CIF005833 --run-label H6_Ge3BiO3 2>&1","tool":"exec_command"},{"arguments_sha256":"cfdbeb9e6134a461c22e6d12a68794bff12c206a6c94157d6a8c308c96029193","files":[],"index":29,"summary":"{\"chars\":\"\",\"session_id\":56152,\"yield_time_ms\":180000}","tool":"write_stdin"},{"arguments_sha256":"794431caa676a0711b009c911d53fbf35cdd06ee03e2ec4d2f3095c24b6169b3","files":[],"index":30,"summary":"cat > /workspace/output/analysis.json << 'ANALYSIS_EOF'\n{\n  \"case_id\": \"DEV102\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF005859\",\n      \"formula\": \"Ge(Bi3O5)4\",\n      \"evidence\": \"Top-ranked ternary phase in screening (fom 0.50). Cubic I23, cell a=10.1586 A (shift +0.13% from CIF). Largest contributor at 36.99 wt%. Only candidate with this formula.\"\n    },\n    {\n      \"candidate_id\": \"CIF005806\",\n      \"formula\": \"GeO2\",\n      \"evidence\": \"Pinned precursor phase. P3_121 trigonal polymorph ","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":31,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"95c78bb099fb51dd7032783f292fd14b8b75a805d02ce84825cd654e2d68acba","files":[],"index":32,"summary":"cat /workspace/output/analysis.json 2>/dev/null || echo \"NOT FOUND\"","tool":"exec_command"},{"arguments_sha256":"f69ee9af7015e1c4156bb5e2505b37396ca6ca5979e641ae436224ad6232d2cd","files":[],"index":33,"summary":"ls -la /workspace/output/H2_Bi2O3_v2/ && echo \"---\" && cat /workspace/output/H2_Bi2O3_v2/result.json","tool":"exec_command"},{"arguments_sha256":"f6e73091b4e25d3e7579c960937a8a84b9bd8ba040dae84e757e30b7eaf876cb","files":[],"index":34,"summary":"cd /workspace && python3 /workspace/physics/screen.py --case DEV102 --residual H2_Bi2O3_v2 2>&1 | head -80","tool":"exec_command"},{"arguments_sha256":"c06b2a5621eac1c9add863bb5f2dc4582f9fc8d0573c1ab80f3554c474c31090","files":[],"index":35,"summary":"cd /workspace && python3 /workspace/physics/candidates.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"90c0975582fdb8057492a5d392a5adb19e967440558c5b320bd9fac4d5453e7c","files":[],"index":36,"summary":"python3 << 'PYEOF'\nimport csv\n\n# Read the rietveld.csv difference curve\ndata = []\nwith open('/workspace/output/H2_Bi2O3_v2/rietveld.csv') as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    for row in reader:\n        data.append([float(x) for x in row])\n\n# Find largest residuals (positive and negative)\ndiffs = [(row[0], row[3]) for row in data]  # 2theta, difference\npositive = sorted([(t, d) for t, d in diffs if d > 0], key=lambda x: -x[1])[:10]\nnegative = sorted([(t, d) for t, d in d","tool":"exec_command"},{"arguments_sha256":"6037c6811ae285af37de7605b3218490dfe667e76d7c4ec263da901a294e0c04","files":[],"index":37,"summary":"cd /workspace && python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001780 CIF005859 CIF005843 --run-label H7_Bi2O3_Pn3m 2>&1","tool":"exec_command"},{"arguments_sha256":"f3058929cf2ee7283799adfe6e2a9e19bdca7bfee5e07fb3f456da619ec45fa6","files":[],"index":38,"summary":"{\"chars\":\"\",\"session_id\":43330,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"081173b62f1a109f0d1b51a03402cb4878e8392b5d3c8c591e05dc43f61bba65","files":[],"index":39,"summary":"{\"chars\":\"\",\"session_id\":43330,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"b6443427518a59eea4250e6b6f3898df4e8cd89e4a0b0372f9ef09273040f585","files":[],"index":40,"summary":"cd /workspace && python3 /workspace/physics/refine.py --case DEV102 --candidates CIF005806 CIF001783 CIF005859 CIF005843 CIF005834 --run-label H8_5phase 2>&1","tool":"exec_command"},{"arguments_sha256":"a133c36f4c04e611167ca928781d8b697de66ec89d2d2aa1c78d3ba435215e81","files":[],"index":41,"summary":"{\"chars\":\"\",\"session_id\":19848,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"a133c36f4c04e611167ca928781d8b697de66ec89d2d2aa1c78d3ba435215e81","files":[],"index":42,"summary":"{\"chars\":\"\",\"session_id\":19848,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"a133c36f4c04e611167ca928781d8b697de66ec89d2d2aa1c78d3ba435215e81","files":[],"index":43,"summary":"{\"chars\":\"\",\"session_id\":19848,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"a133c36f4c04e611167ca928781d8b697de66ec89d2d2aa1c78d3ba435215e81","files":[],"index":44,"summary":"{\"chars\":\"\",\"session_id\":19848,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"03b3772b7f9ce61d245fa11500ed5b12350ab2284811defd24f3098b85fb386e","files":[],"index":45,"summary":"python3 << 'PYEOF'\n# Compute Bi:Ge atomic ratio from refined weight fractions\n# Using the formulas:\n# Ge(Bi3O5)4 = GeBi12O20 -> Ge:1, Bi:12, O:20 -> MW = 72.63 + 12*208.98 + 20*16.00\n# GeO2 -> Ge:1, O:2 -> MW = 72.63 + 2*16.00\n# Bi2O3 -> Bi:2, O:3 -> MW = 2*208.98 + 3*16.00\n# GeBi2O5 -> Ge:1, Bi:2, O:5 -> MW = 72.63 + 2*208.98 + 5*16.00\n\n# Atomic weights\nGe = 72.63\nBi = 208.98\nO = 16.00\n\n# Molecular weights\nMW_GeBi3O5_4 = Ge + 12*Bi + 20*O  # Ge(Bi3O5)4 = GeBi12O20\nMW_GeO2 = Ge + 2*O\nMW_Bi2O3 = ","tool":"exec_command"},{"arguments_sha256":"499597e045452f6e8768b01a5a6fab396dc9f97ac5ead50d9c9b52906d0e0110","files":[],"index":46,"summary":"ls -la /workspace/output/ && echo \"---\" && for d in /workspace/output/*/; do echo \"=== $d ===\" && head -5 \"$d/result.json\" 2>/dev/null && python3 -c \"\nimport json\nwith open('$d/result.json') as f:\n    r = json.load(f)\n# Get last stage\nstages = ['rietveld', 'rietveld_profile', 'rietveld_lattice', 'pawley']\nfor s in stages:\n    if s in r:\n        print(f'  {s}: Rwp={r[s][\\\"rwp\\\"]}% GoF={r[s][\\\"gof\\\"]:.2f} conv={r[s][\\\"converged\\\"]}')\n        if 'phases' in r[s]:\n            for p in r[s]['phases']","tool":"exec_command"},{"arguments_sha256":"97d80cc9835262eddafc87146feb39d15781b166c4b55b7ce3ef0e426346308a","files":[],"index":47,"summary":"python3 << 'PYEOF'\nimport json\nwith open('/workspace/output/H3_GeBi2O5_pnma/result.json') as f:\n    r = json.load(f)\n# Print all keys\nfor key in r:\n    if key in ['pawley', 'rietveld', 'rietveld_lattice', 'rietveld_profile']:\n        print(f\"Stage '{key}' present: {key in r}\")\n    else:\n        print(f\"{key}: {r[key]}\")\nPYEOF","tool":"exec_command"},{"arguments_sha256":"db5179404d3bcb2ff11b6b299ff08c34c1a303d9be54fff984f54caa2199ac2c","files":[],"index":48,"summary":"python3 << 'PYEOF'\nimport json\nwith open('/workspace/output/H2_Bi2O3_v2/result.json') as f:\n    r = json.load(f)\n\n# Print final rietveld stage details\nstage = r['rietveld']\nprint(\"=== Final Rietveld Stage (H2) ===\")\nprint(f\"Rwp: {stage['rwp']}%\")\nprint(f\"Rp: {stage['rp']}%\")\nprint(f\"Rpb: {stage['rpb']}%\")\nprint(f\"Rexp: {stage['rexp']}%\")\nprint(f\"GoF: {stage['gof']}\")\nprint(f\"Durbin-Watson: {stage['durbin_watson']}\")\nprint(f\"Converged: {stage['converged']}\")\nprint(f\"Iterations: {stage['iteration_","tool":"exec_command"},{"arguments_sha256":"d9d865c8e384dc0955676fbd6d98657578bdd82c30363d49f98dfad41072df0f","files":[],"index":49,"summary":"python3 << 'PYEOF'\nimport json\nwith open('/workspace/output/H2_Bi2O3_v2/result.json') as f:\n    r = json.load(f)\n\nfor stage_name in ['pawley', 'rietveld_lattice', 'rietveld_profile', 'rietveld']:\n    s = r[stage_name]\n    print(f\"\\n=== {stage_name} (Rwp={s['rwp']}%) ===\")\n    for p in s['phases']:\n        print(f\"  {p['phase_id']}: wt={p['weight_fraction']:.4f}%, wt_err={p['weight_fraction_error']}\")\nPYEOF","tool":"exec_command"},{"arguments_sha256":"fa01e93f074eaa1bc52b9cd638a8d6605a378820fe2a0f820059103cdbd7de1b","files":[],"index":50,"summary":"ls /workspace/output/ 2>/dev/null && echo \"---\" && cat /workspace/output/analysis.json 2>/dev/null | head -100","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":51,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"42ca51ccd15b42356f8340e510de991b02f8f323e4bbdf8c8f65d77cb792b9eb","files":[],"index":52,"summary":"cat /workspace/output/H2_Bi2O3_v2/result.json","tool":"exec_command"},{"arguments_sha256":"bf5ed63bf8ea59328d2a10c473bfbef8d56cb53ffa9e8743f3c8705141dd2546","files":[],"index":53,"summary":"for d in H1_search H3_GeBi2O5_pnma H4_no_GeBi2O5 H5_GeO2_pbcn H6_Ge3BiO3 H7_Bi2O3_Pn3m H8_5phase; do\n  echo \"=== $d ===\"\n  python3 -c \"\nimport json\nwith open('/workspace/output/$d/result.json') as f:\n    r = json.load(f)\nif 'rietveld' in r:\n    st = r['rietveld']\n    print(f'  Rwp={st[\\\"rwp\\\"]}%, GoF={st[\\\"gof\\\"]:.3f}, conv={st[\\\"converged\\\"]}, DW={st[\\\"durbin_watson\\\"]}')\n    for p in st['phases']:\n        print(f'    {p[\\\"phase_id\\\"]}: {p[\\\"weight_fraction\\\"]:.1f}% (wt_err={p[\\\"weight_fraction","tool":"exec_command"},{"arguments_sha256":"dd42a51e5689da48deec1c5fafc51e509abbf6c63c3a99a1fb556207a8ec9483","files":[],"index":54,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H3_GeBi2O5_pnma/result.json') as f:\n    r = json.load(f)\nprint('Keys:', list(r.keys()))\nprint('pawley' in r, 'rietveld' in r)\nif 'pawley' in r and r['pawley']:\n    p = r['pawley']\n    print(f'Pawley Rwp={p[\\\"rwp\\\"]}%, GoF={p[\\\"gof\\\"]:.3f}, conv={p[\\\"converged\\\"]}')\nelse:\n    print('No pawley stage or None')\n\"","tool":"exec_command"},{"arguments_sha256":"13e35938e3d3cdffbda67e590ad87275ec852d8b5513c3c6ba3acf4b28942740","files":[],"index":55,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H3_GeBi2O5_pnma/result.json') as f:\n    r = json.load(f)\nst = r['rietveld']\nprint(f'Rwp={st[\\\"rwp\\\"]}%, GoF={st[\\\"gof\\\"]:.3f}, conv={st[\\\"converged\\\"]}')\nfor p in st['phases']:\n    print(f'  {p[\\\"phase_id\\\"]}: {p[\\\"weight_fraction\\\"]:.1f}%')\n\"","tool":"exec_command"},{"arguments_sha256":"b54be780ea30894cc907b114818526e7a468295d095f887fc129faa613deccfc","files":[],"index":56,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H3_GeBi2O5_pnma/result.json') as f:\n    r = json.load(f)\nprint('rietveld stage:', r['rietveld'])\nprint('rietveld_lattice stage:', r['rietveld_lattice'] is not None)\nprint('rietveld_profile stage:', r['rietveld_profile'] is not None)\nprint('pawley GoF:', r['pawley']['gof'])\nprint('pawley converged:', r['pawley']['converged'])\nprint('degradation:', r['stage_degradation'])\n\"","tool":"exec_command"},{"arguments_sha256":"f688c6817f27d3f04ad5996da3d7b024cfe228d12296af34c4fc3d157cf76840","files":[],"index":57,"summary":"python3 << 'PYEOF'\n# Compute Bi:Ge atomic ratio from refined weight fractions\n# CIF005859: Ge(Bi3O5)4 -> Ge1 Bi12 O20 (M = 72.63 + 12*208.98 + 20*16.00 = 72.63 + 2507.76 + 320.00 = 2900.39 g/mol)\n# CIF005806: GeO2 -> Ge1 O2 (M = 72.63 + 32.00 = 104.63 g/mol)  \n# CIF001783: Bi2O3 -> Bi2 O3 (M = 2*208.98 + 48.00 = 465.96 g/mol)\n# CIF005843: GeBi2O5 -> Ge1 Bi2 O5 (M = 72.63 + 2*208.98 + 80.00 = 570.59 g/mol)\n\nformulas = {\n    'CIF005859': {'Ge': 1, 'Bi': 12, 'O': 20, 'M': 72.63 + 12*208.98 + 20*16.","tool":"exec_command"},{"arguments_sha256":"77b5c1f4e45fca955b60f1a6c81f37c95dd37fecb636a8a0296b56fa11820cdc","files":[],"index":58,"summary":"python3 /workspace/physics/case_brief.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"d3505ed3afbef1397bbcde8d693079513a4dfac23a8272638974c586dd324216","files":[],"index":59,"summary":"python3 /workspace/physics/candidates.py --case DEV102 2>&1","tool":"exec_command"},{"arguments_sha256":"9b7f7923110540a8fdc8923c8c224f276852ac9ad4671df03d190cac54cc61cc","files":[],"index":60,"summary":"python3 << 'PYEOF'\nimport csv\nimport numpy as np\n\n# Read the final rietveld curve\nwith open('/workspace/output/H2_Bi2O3_v2/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    rows = list(reader)\n\ntwo_theta = np.array([float(r['two_theta']) for r in rows])\nobserved = np.array([float(r['observed']) for r in rows])\ncalculated = np.array([float(r['calculated']) for r in rows])\ndifference = np.array([float(r['difference']) for r in rows])\n\n# Find max positive and negative differences\n# First, nor","tool":"exec_command"},{"arguments_sha256":"34e575d0c6cf2a8f70a3870988fd639484ff24e1d6506d5cadbc48ddaa92ef2e","files":[],"index":61,"summary":"python3 << 'PYEOF'\nimport csv\nimport numpy as np\n\nwith open('/workspace/output/H2_Bi2O3_v2/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    rows = list(reader)\n\ntwo_theta = np.array([float(r['two_theta']) for r in rows])\nobserved = np.array([float(r['observed']) for r in rows])\ncalculated = np.array([float(r['calculated']) for r in rows])\ndifference = np.array([float(r['difference']) for r in rows])\n\nmax_obs = np.max(observed)\nnorm_diff = (difference / max_obs) * 100\n\n# Largest positive r","tool":"exec_command"},{"arguments_sha256":"25d0876c9bcc478fbd374e3a7bee8b6330f95e6b2acea30c0664854f221974b7","files":[],"index":62,"summary":"python3 << 'PYEOF'\n# Mass loss: 2004mg precursors (but brief says 1.38156g + 0.62231g = 2.00387g = 2003.87mg)\n# mass_recovered = 461mg\nmass_precursors = 1.38156 + 0.62231  # grams\nmass_recovered = 0.461  # grams\nloss_pct = (1 - mass_recovered / mass_precursors) * 100\nprint(f\"Mass precursors: {mass_precursors:.4f}g = {mass_precursors*1000:.1f}mg\")\nprint(f\"Mass recovered: {mass_recovered:.3f}g = {mass_recovered*1000:.0f}mg\")\nprint(f\"Mass loss: {loss_pct:.1f}%\")\n\n# Check the Bi:Ge ratio from precur","tool":"exec_command"},{"arguments_sha256":"710c98037e33db02e17fedc68f4859e620ce5e5367c2091f89fd3c7c9a38e053","files":[],"index":63,"summary":"python3 /workspace/physics/screen.py --case DEV102 --residual H2_Bi2O3_v2 --no-search 2>&1","tool":"exec_command"},{"arguments_sha256":"69c8b529b78eb8bcdc132ed5e88ffa617106323477bd10e04d3ad1a19271c6ec","files":[],"index":64,"summary":"cat > /workspace/output/analysis.json << 'JSONEOF'\n{\n  \"case_id\": \"DEV102\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF005859\",\n      \"formula\": \"Ge(Bi3O5)4\",\n      \"evidence\": \"Top-ranked ternary phase in screening (fom 0.50). Cubic I23, cell a=10.1586 A (shift +0.13% from CIF). Largest contributor at 36.99 wt%. Only candidate with this formula.\"\n    },\n    {\n      \"candidate_id\": \"CIF005806\",\n      \"formula\": \"GeO2\",\n      \"evidence\": \"Pinned precursor phase. P3_121 trigonal polymorph ranke","tool":"exec_command"},{"arguments_sha256":"78282e1af20bb982da6cc360ecff0d511c12dc28fcf3c21015fb241e29f027fa","files":[],"index":65,"summary":"python3 << 'PYEOF'\nimport json\nwith open('/workspace/output/analysis.json') as f:\n    data = json.load(f)\n\n# Check weight fractions sum to 1.0\nwf = data['weight_fractions']\ntotal = sum(wf.values())\nprint(f\"Weight fractions sum: {total:.4f}\")\nprint(f\"Phases: {len(data['phases'])}\")\n\n# Verify no fabricated ESDs in uncertainties\nunc = data['uncertainties']\nprint(f\"\\nQuantitative uncertainty mentions 'null' or 'covariance-based' or 'no': {any(kw in unc['quantitative'].lower() for kw in ['null', 'cov","tool":"exec_command"}],"wall_seconds":2687.061846},"status":"completed"},"parent":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","rationale":"","root":"380fd7e029f3fa616bdf3615d1dce18f3329b106e2ccdaaf3c4698cad4d7676f","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"71c12f9a1ab1f1d7b825347adbfbd88f1b3c5674c8afd352e27e9c83ac01d6ad","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"296c68d82e55a032d5e18c1fbbf92a5cb9c4c9ef8363a8d5a3de92a469d79a7f","size_bytes":834185,"stage":"rietveld"},"gof":1.8875,"phases":[{"candidate_id":"CIF005806","cell":{"a":4.9861699999999995,"alpha":90.0,"b":4.9861699999999995,"beta":90.0,"c":5.6466400000000005,"gamma":90.0},"spacegroup_no":152,"weight_percent":31.60890872864901,"weight_percent_error":0.22},{"candidate_id":"CIF001783","cell":{"a":5.850499999999999,"alpha":90.0,"b":8.16934,"beta":112.981,"c":7.51277,"gamma":90.0},"spacegroup_no":14,"weight_percent":18.9236742258783,"weight_percent_error":0.18},{"candidate_id":"CIF005859","cell":{"a":10.1586,"alpha":90.0,"b":10.1586,"beta":90.0,"c":10.1586,"gamma":90.0},"spacegroup_no":197,"weight_percent":36.98706188370631,"weight_percent_error":0.18},{"candidate_id":"CIF005843","cell":{"a":15.6937,"alpha":90.0,"b":5.5056899999999995,"beta":90.0,"c":5.39176,"gamma":90.0},"spacegroup_no":36,"weight_percent":12.480355161766376,"weight_percent_error":0.16}],"quantification":"quantitative","rwp_percent":6.04,"stage":"rietveld"},"fit_basis":"71c12f9a1ab1f1d7b825347adbfbd88f1b3c5674c8afd352e27e9c83ac01d6ad","fit_origin":"imported","material_sha256":"a8bad9935d65636576c8ae464a0d0118f23f7bfac9b6714e85dec656c6fd1966","measurement_sha256":"0f20379631b26f6f0e199c1c4f7214021eae920447deaba557cce6260bb1727d","phases":["CIF005859","CIF005806","CIF001783","CIF005843"]},"material":{"declared_target":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger target_compound"},"value":"Ge2Bi2O7"},"declared_target_stoichiometry":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger target_stoichiometry"},"value":"Bi2O3-2GeO2"},"elements":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"elements of the declared precursors"},"value":["Bi","Ge","O"]},"elements_basis":"declared","precursors":[{"amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_actual_masses"},"value":{"unit":"g","value":1.38156}},"cas_number":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].cas_number"},"value":"1304-76-3"},"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].formula"},"value":"Bi2O3"},"name":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].name"},"value":"bismuth(iii) oxide"},"purity":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[0].sa_purity"},"value":0.9990000000000001},"target_amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_target_masses"},"value":{"unit":"g","value":1.38014}}},{"amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_actual_masses"},"value":{"unit":"g","value":0.62231}},"cas_number":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].cas_number"},"value":"1310-53-8"},"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].formula"},"value":"GeO2"},"name":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].name"},"value":"germanium(iv) oxide"},"purity":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger sample.precursors[1].sa_purity"},"value":0.9999800000000001},"target_amount":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.precursor_target_masses"},"value":{"unit":"g","value":0.61986}}}],"processing":[{"atmosphere":null,"cooling":null,"cooling_rate_c_per_min":null,"duration_min":null,"equipment":null,"furnace":null,"heating_rate_c_per_min":null,"mass_mg":null,"met_target_mass":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.met_target_mass"},"value":true},"operation":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger workflow_spec.steps[PowderDosing].action"},"value":"dose"},"order":1,"temperature_c":null,"temperature_profile":null},{"atmosphere":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger not recorded: the ledger has no atmosphere field"},"value":null},"cooling":null,"cooling_rate_c_per_min":null,"duration_min":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger synthesis.heating_time"},"value":60.0},"equipment":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"dataset_metadata","document":"a40a2b324b1a3d93659c2ffc89a2d73fe4c25fa0a66aa9e818bbc0e9f68405b3","kind":"document","locator":"precursor_genome ledger 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They replace the shell commands named above.\n\n- `case_brief()` runs `case_brief.py --case DEV006`.\n- `candidates()` runs `candidates.py --case DEV006`.\n- `screen(residual=null)` runs `screen.py --case DEV006 --no-search`, or `--residual <run_label>` when you pass one.\n- `refine(candidates, run_label, pawley_only=false)` runs `refine.py --case DEV006 --candidates ... --run-label <label>`. A label cannot be reused.\n- `write_analysis(analysis)` writes your answer to `/workspace/output/analysis.json`.\n\nThe answer is a JSON object with `case_id` (\"DEV006\"), `phases` (a list of objects, each with `candidate_id` from the candidate library), `weight_fractions` (an object from candidate_id to a number from 0 to 1), and `fit_artifacts` (paths of the fit files the answer rests on, such as `/workspace/output/<run_label>/result.json`). Cite the refine run whose candidates are exactly your answered phases. Write the answer before you stop. 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/workspace/output/H1_alt_bio3/result.json","tool":"exec_command"},{"arguments_sha256":"ff5400fa1cb3cbd28e69f772c7c3bdd7d356ded09b7ae8e776137805d70dc3c9","files":[],"index":18,"summary":"cat /workspace/output/H1_precursors/result.json | python3 -c \"\nimport json, sys\nr = json.load(sys.stdin)\nprint('=== CIF001779 (H1_precursors) ===')\nfor p in r['rietveld']['phases']:\n    print(f\\\"  {p['phase_id']}: wt%={p['weight_fraction']:.2f}, cell={p['lattice_params']}\\\")\nprint(f\\\"  Rwp={r['rietveld']['rwp']}, GoF={r['rietveld']['gof']:.3f}\\\")\nr2 = json.load(open('/workspace/output/H1_alt_bio3/result.json'))\nprint('=== CIF001783 (H1_alt_bio3) ===')\nfor p in r2['rietveld']['phases']:\n    print","tool":"exec_command"},{"arguments_sha256":"57c36bfc1c4fdb5cc75a5a456ca446f1777c5d852379398fd894357fd9f6a5ae","files":[],"index":19,"summary":"mkdir -p /workspace/output && cat > /workspace/output/analysis.json << 'ANALYSIS_EOF'\n{\n  \"case_id\": \"DEV006\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF012075\",\n      \"formula\": \"NiO\",\n      \"evidence\": \"Declared precursor NiO. Ranked #4-7 in screening (fom 0.44, full coverage). Rietveld refinement confirms cubic Fm-3m structure with refined cell a=4.1786 A (+0.25% from CIF). Weight fraction 38.0+/-0.7 wt%. Part of search hypothesis H1 (Rwp 6.71%) confirmed by full refinement.\"\n    },\n    {","tool":"exec_command"},{"arguments_sha256":"c9f625e6030cd00039cfbea71242eb1ca0e97bac85c13ca2d5e2679ee93f6d11","files":[],"index":20,"summary":"cd /workspace && python3 << 'PYEOF'\nimport csv, numpy as np\n\n# Read the rietveld.csv difference curve\nwith open(\"/workspace/output/H1_alt_bio3/rietveld.csv\") as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    data = list(reader)\n\ntwo_theta = np.array([float(r[0]) for r in data])\nobserved = np.array([float(r[1]) for r in data])\ncalculated = np.array([float(r[2]) for r in data])\ndifference = np.array([float(r[3]) for r in data])\n\n# Find the noise level (robust std of difference in flat","tool":"exec_command"},{"arguments_sha256":"992e8ea864ecc79d30067db01e64be297b78d8d252d51af85c54a3bd99eb376f","files":[],"index":21,"summary":"cd /workspace && python3 physics/refine.py --case DEV006 --candidates CIF012075 CIF008546 CIF001783 --run-label H2_hex_li2co3","tool":"exec_command"},{"arguments_sha256":"c835576914891562234b952e5f008dd66e8982a9aa0dfd25cf02eac6a2e39bda","files":[],"index":22,"summary":"{\"chars\":\"\",\"session_id\":9310,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"e7a90fdf5bcc4a6e2e38a580c0a458f3337cb1930012fbbe04c67af618ffd1d9","files":[],"index":23,"summary":"cd /workspace && python3 << 'PYEOF'\nimport csv, numpy as np\n\nwith open(\"/workspace/output/H1_alt_bio3/rietveld.csv\") as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    data = list(reader)\n\ntwo_theta = np.array([float(r[0]) for r in data])\nobserved = np.array([float(r[1]) for r in data])\ncalculated = np.array([float(r[2]) for r in data])\ndifference = np.array([float(r[3]) for r in data])\n\n# Look at 26-29 deg region\nmask = (two_theta > 26) & (two_theta < 29)\nprint(\"Region 26-29 deg (ne","tool":"exec_command"},{"arguments_sha256":"68790b602e965bba7abcc1c6a5fb2baf8c23604852bca2f0b7cb33fcdc9bf51a","files":[],"index":24,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":25,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"c11a466cbdd11094d72b1f9b89170e28770f106ac0b0c48c92c68ee00da8040f","files":[],"index":26,"summary":"ls -la /workspace/output/","tool":"exec_command"},{"arguments_sha256":"a9763100ff182ccee79e1d7f942570487bedac1a8bc932644f934f96f99524aa","files":[],"index":27,"summary":"cat /workspace/output/H1_alt_bio3/result.json","tool":"exec_command"},{"arguments_sha256":"db06c95acdb959e3b4fa09a02be929b87c3788f2f6b0a53686850f2eb26ff945","files":[],"index":28,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV006 --residual H1_alt_bio3","tool":"exec_command"},{"arguments_sha256":"4b403ba532c83fd8aff57c21307e54b3abee656398566a6f4e00c0742246c582","files":[],"index":29,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":13303,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"2b550202f40aa4f30f8116090f1e7d406ed2c12e174ae0ac34b6e3decfde5f55","files":[],"index":30,"summary":"cd /workspace && python3 /workspace/physics/candidates.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"bae1e28909e2abe07fb7085cdc089cb5cd5e2832f7607b6c5c1aed7ad1682a1f","files":[],"index":31,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":51871,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"309efe3583f4f6302f66715ca45621c697f6106b86241eab5a06f29711a4dada","files":[],"index":32,"summary":"head -5 /workspace/output/H1_alt_bio3/rietveld.csv && echo \"---\" && wc -l /workspace/output/H1_alt_bio3/rietveld.csv","tool":"exec_command"},{"arguments_sha256":"83ac55a9397d6ca5314ee5e3c8b3cb66eb9c2a4866a47937907e63a0e80b3bb8","files":[],"index":33,"summary":"python3 -c \"\nimport csv\n\n# Read the rietveld CSV\nwith open('/workspace/output/H1_alt_bio3/rietveld.csv') as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    rows = [(float(r[0]), float(r[1]), float(r[2]), float(r[3])) for r in reader]\n\n# Find max observed\nmax_obs = max(r[1] for r in rows)\nprint(f'Max observed: {max_obs}')\n\n# Print regions of interest\nregions = [\n    (21.3, 21.5, '21.39 pos res'),\n    (23.8, 24.1, '23.96 pos res'),\n    (27.0, 27.9, '27.3-27.7 neg res'),\n    (30.5, 31.0","tool":"exec_command"},{"arguments_sha256":"528070f0b64b09ead2e3d4b81424ab776123b355eb1e275c917dd1c140688cc4","files":[],"index":34,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012076 COD2310703 CIF001783 --run-label H3_NiO76","tool":"exec_command"},{"arguments_sha256":"41247ebc2fdf2d317fe2ab618ae2ceae55ef463ec8b9a01409dd671574e87972","files":[],"index":35,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":3380,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"1a62c9f3ee513c5f014cd795d4b3b112b284e159b051326f8913c2e0b7244a58","files":[],"index":36,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":3380,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"1a62c9f3ee513c5f014cd795d4b3b112b284e159b051326f8913c2e0b7244a58","files":[],"index":37,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":3380,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"551b621a6393f4532096f35cc19ddee5c66233fb5246cb83b18541b9e26b2bc8","files":[],"index":38,"summary":"python3 -c \"\nimport csv\n\n# Compare residuals at 43 deg region for both fits\nfor label, path in [('H1_alt_bio3 (NiO CIF012075)', '/workspace/output/H1_alt_bio3/rietveld.csv'),\n                     ('H3_NiO76 (NiO CIF012076)', '/workspace/output/H3_NiO76/rietveld.csv')]:\n    print(f'=== {label} ===')\n    with open(path) as f:\n        reader = csv.reader(f)\n        next(reader)\n        for r in reader:\n            tt, obs, calc, diff = float(r[0]), float(r[1]), float(r[2]), float(r[3])\n            ","tool":"exec_command"},{"arguments_sha256":"991a10c3cc26fb319cd6eaa64732496a46f60a70d6f9d53749a8a5e93260669b","files":[],"index":39,"summary":"cd /workspace && python3 /workspace/physics/case_brief.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"4bdae87ef039ee84b5cb644348959ee02a9b4615c6fa04a9ce30330d67b5baf4","files":[],"index":40,"summary":"cat /workspace/input/manifest.json","tool":"exec_command"},{"arguments_sha256":"de6383c16b087158d71509f12d2aa6e2232ba4c86fc7335faff53c82c9eb4321","files":[],"index":41,"summary":"ls -la /workspace/output/ 2>/dev/null; echo \"---\"; ls -la /workspace/output/H1_alt_bio3/ 2>/dev/null; echo \"---\"; ls -la /workspace/output/H3_NiO76/ 2>/dev/null; echo \"---\"; cat /workspace/output/analysis.json 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"88ef3c9919edc5700821b0f571cfb85af0f485c8cacd767c3d79d4d1156c46bc","files":[],"index":42,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H1_alt_bio3/result.json') as f:\n    d = json.load(f)\nprint('=== KEY STATS ===')\nprint('rwp:', d.get('rwp'))\nprint('rp:', d.get('rp'))\nprint('rpb:', d.get('rpb'))\nprint('rexp:', d.get('rexp'))\nprint('gof:', d.get('gof'))\nprint('durbin_watson:', d.get('durbin_watson'))\nprint()\nprint('=== PHASE WEIGHTS ===')\nfor p in d.get('phases', []):\n    print(p.get('candidate_id'), p.get('formula'), 'weight_fraction:', p.get('weight_fraction'), 'weight_frac","tool":"exec_command"},{"arguments_sha256":"24ba39b189b004e68a6dd521dad4888cf6a3e1588b2172bdc1dbfc66b5d3f361","files":[],"index":43,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H1_alt_bio3/result.json') as f:\n    d = json.load(f)\nprint('Top-level keys:', list(d.keys()))\nfor k in d.keys():\n    print(f'  {k}: {type(d[k]).__name__}', str(d[k])[:200])\n\"\n","tool":"exec_command"},{"arguments_sha256":"212224afe7b354fcdf2d9c214685ca7185623668ec10b4a29f52271601169692","files":[],"index":44,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/H1_alt_bio3/result.json') as f:\n    d = json.load(f)\n\nr = d['rietveld']\nprint('=== FINAL RIETVELD STAGE ===')\nprint('rwp:', r.get('rwp'))\nprint('rp:', r.get('rp'))\nprint('rpb:', r.get('rpb'))\nprint('rexp:', r.get('rexp'))\nprint('gof:', r.get('gof'))\nprint('durbin_watson:', r.get('durbin_watson'))\nprint('sum_weight_fractions:', r.get('sum_weight_fractions'))\nprint()\n\nprint('=== PHASES ===')\nfor p in r.get('phases', []):\n    print(f\\\"\\\"\\\"\n  pha","tool":"exec_command"},{"arguments_sha256":"e61219f29786245e2525973a039b396a169622f3a603210d2bc3bdc4e6d4ab84","files":[],"index":45,"summary":"python3 -c \"\nimport json\nfor run in ['H1_precursors', 'H2_hex_li2co3', 'H3_NiO76']:\n    path = f'/workspace/output/{run}/result.json'\n    with open(path) as f:\n        d = json.load(f)\n    r = d['rietveld']\n    sd = d['stage_degradation']\n    print(f'=== {run} ===')\n    print(f'  Pawley Rwp: {sd[\\\"pawley_rwp\\\"]}  Final Rwp: {r[\\\"rwp\\\"]}  GoF: {r[\\\"gof\\\"]}')\n    print(f'  Degraded: {sd[\\\"rietveld_degraded_after_good_pawley\\\"]}')\n    for p in r['phases']:\n        print(f'  {p[\\\"phase_id\\\"]}: {p[\\\"","tool":"exec_command"},{"arguments_sha256":"fa938d9db7bdd51b116ea8a8c0110a5c77ca16ab48545659a939bc92e59a7bc4","files":[],"index":46,"summary":"python3 /workspace/physics/case_brief.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"0df8b60436f6a304f45865e59a8d765d082279e328514e874a910ca32848c791","files":[],"index":47,"summary":"python3 /workspace/physics/candidates.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"3e10f89324eeb3793e25019e40716d9e8065f98e687953d35ebe1ad170be560b","files":[],"index":48,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":16310,\"yield_time_ms\":15000}","tool":"write_stdin"},{"arguments_sha256":"9011324cb72071da5b84f18323b58ff51e477368d566a9af11c9f4c5296857f0","files":[],"index":49,"summary":"find /workspace/output -name \"screen*\" -o -name \"*.csv\" -o -name \"H1_alt_bio3/request.json\" | head -20; echo \"---\"; cat /workspace/output/H1_alt_bio3/request.json","tool":"exec_command"},{"arguments_sha256":"bf671e312c21b2dcc6570d3cd73afc2241920dd47d73b000c029b34336dd653f","files":[],"index":50,"summary":"python3 -c \"\nimport csv\n# Read the rietveld.csv to check residuals\ndata = []\nwith open('/workspace/output/H1_alt_bio3/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    headers = reader.fieldnames\n    print('Headers:', headers)\n    for row in reader:\n        data.append(row)\nprint(f'Total points: {len(data)}')\nprint()\n\n# Find max observed\nobs = float(data[0]['observed'])\nmax_obs = 0\nfor row in data:\n    v = abs(float(row['observed']))\n    if v > max_obs:\n        max_obs = v\nprint(f'Max obse","tool":"exec_command"},{"arguments_sha256":"dd54c58579fb6d225a969c31437da9734196f233cb2b7c45a6a3be1b59385aa6","files":[],"index":51,"summary":"python3 -c \"\nimport csv\ndata = []\nwith open('/workspace/output/H1_alt_bio3/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    for row in reader:\n        data.append(row)\n\n# Check around 32.76\nprint('=== Around 32.76 deg ===')\nfor row in data:\n    tt = float(row['two_theta'])\n    if 32.6 <= tt <= 32.9:\n        obs = float(row['observed'])\n        calc = float(row['calculated'])\n        diff = float(row['difference'])\n        if abs(diff) > 50:\n            print(f'  2theta={tt:.4f}  obs={obs:","tool":"exec_command"},{"arguments_sha256":"e454c9480926be93708990946e675b012753f2fc03f29fa8c3bf0708961f639f","files":[],"index":52,"summary":"ls /workspace/input/ /workspace/input/candidates/DEV006/","tool":"exec_command"},{"arguments_sha256":"3fb0b50aa95cae5d33a7e737605a6794a484ba4b1e936109feb0615a6108c294","files":[],"index":53,"summary":"python3 -c \"\nimport numpy as np\n\n# Calculate d-spacings and 2theta for known peaks\nlam = 1.5406  # Cu Ka1 in Angstrom\n\ndef d_to_2th(d):\n    return 2 * np.degrees(np.arcsin(lam / (2*d)))\n\n# Check Li2O (Fm-3m, a=4.728) - CIF008890\na = 4.728\nfor h,k,l in [(1,1,1), (2,0,0), (2,2,0), (3,1,1), (2,2,2)]:\n    d = a / np.sqrt(h**2 + k**2 + l**2)\n    if d > 0 and lam/(2*d) <= 1:\n        print(f'Li2O({h}{k}{l}): d={d:.3f} 2th={d_to_2th(d):.2f}')\n\nprint()\n\n# Check Bi2CO5 (Pna2_1, a=5.468, b=27.320, c=?)\n# J","tool":"exec_command"},{"arguments_sha256":"00305a0221ab7224a826b4084a2d882e72d8107beebf38255935b42b6761b520","files":[],"index":54,"summary":"python3 -c \"\nimport numpy as np\n\nlam = 1.5406\n\ndef d_to_2th(d):\n    return 2 * np.degrees(np.arcsin(lam / (2*d)))\n\n# NiO (Fm-3m, a=4.179)\na = 4.179\nfor h in range(0,5):\n    for k in range(h,5):\n        for l in range(k,5):\n            if h==0 and k==0 and l==0:\n                continue\n            d = a / np.sqrt(h**2 + k**2 + l**2)\n            tth = d_to_2th(d)\n            if 30 < tth < 35:\n                print(f'NiO({h}{k}{l}): d={d:.3f} 2th={tth:.2f}')\n\nprint()\n\n# Bi2O3 (P2_1/c, a=5.851, b=8","tool":"exec_command"},{"arguments_sha256":"dcb8b75d760a95df7cd75d9d9e71fff87f757e75d333ce89dc0bff1d72606850","files":[],"index":55,"summary":"python3 -c \"\nimport numpy as np\n\nlam = 1.5406\n\ndef d_to_2th(d):\n    return 2 * np.degrees(np.arcsin(lam / (2*d)))\n\n# NiO (Fm-3m, a=4.179)\na = 4.179\nfor h in range(0,5):\n    for k in range(h,5):\n        for l in range(k,5):\n            if h==0 and k==0 and l==0:\n                continue\n            d = a / np.sqrt(h**2 + k**2 + l**2)\n            tth = d_to_2th(d)\n            if 23 < tth < 25:\n                print(f'NiO({h}{k}{l}): d={d:.3f} 2th={tth:.2f}')\n\nprint()\n\n# Bi2O3 (P2_1/c)\na2, b2, c2 =","tool":"exec_command"},{"arguments_sha256":"19ce132e79aca87b621accfa34d78d6b53760b0db86f022eeb8efe36b5804edd","files":[],"index":56,"summary":"python3 -c \"\nimport json\n\n# Read the best fit for exact numbers\nwith open('/workspace/output/H1_alt_bio3/result.json') as f:\n    d = json.load(f)\n\nr = d['rietveld']\nsd = d['stage_degradation']\npaw = d['pawley']\n\n# Extract exact weight fractions\nwf = {}\nfor p in r['phases']:\n    wf[p['phase_id']] = p['weight_fraction']\n\n# Read the CIF files to get space groups\ncifs = {\n    'CIF012075': 'NiO Fm-3m',\n    'COD2310703': 'Li2CO3 C2/c',\n    'CIF001783': 'Bi2O3 P2_1/c'\n}\n\nanalysis = {\n    'case_id': 'DE","tool":"exec_command"},{"arguments_sha256":"bb7e332fcba799e9578dc75d36dfbd845018fcd39a7b0fe0cc8d26ba73f719b8","files":[],"index":57,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"3a265fb5100e31e635268936eb303eb88c02f8ed46a934bcacf13c8bfed22460","files":[],"index":58,"summary":"python3 -c \"\nimport numpy as np\n\nlam = 1.5406\n\ndef d_to_2th(d):\n    return 2 * np.degrees(np.arcsin(lam / (2*d)))\n\n# NiO (Fm-3m, a=4.179)\na = 4.179\nfor h in range(0,5):\n    for k in range(h,5):\n        for l in range(k,5):\n            if h==0 and k==0 and l==0:\n                continue\n            d = a / np.sqrt(h**2 + k**2 + l**2)\n            tth = d_to_2th(d)\n            if 26 < tth < 29:\n                print(f'NiO({h}{k}{l}): d={d:.3f} 2th={tth:.2f}')\n\nprint()\n\n# Bi2O3 (P2_1/c) - check peak","tool":"exec_command"}],"wall_seconds":1363.912489},"status":"completed"},"parent":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","rationale":"","root":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"3671f0cee70cccb951e7bb806c2636f9cd4b9b2d14040579f2847fceeccc8038","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"890c7dca52c635843694d82d2986f6e87f59323d5acffcaf449c4e903a098186","size_bytes":832665,"stage":"rietveld"},"gof":1.8247422680412373,"phases":[{"candidate_id":"CIF012075","cell":{"a":4.178586,"alpha":90.0,"b":4.178586,"beta":90.0,"c":4.178586,"gamma":90.0},"spacegroup_no":225,"weight_percent":38.02961849829797,"weight_percent_error":0.73},{"candidate_id":"COD2310703","cell":{"a":8.424199999999999,"alpha":90.0,"b":4.97617,"beta":115.419,"c":6.233140000000001,"gamma":90.0},"spacegroup_no":15,"weight_percent":39.624289779632036,"weight_percent_error":1.1},{"candidate_id":"CIF001783","cell":{"a":5.85108,"alpha":90.0,"b":8.17144,"beta":112.9789,"c":7.5137,"gamma":90.0},"spacegroup_no":14,"weight_percent":22.34609172206999,"weight_percent_error":0.43}],"quantification":"restricted_profile","rwp_percent":3.54,"stage":"rietveld"},"fit_basis":"3671f0cee70cccb951e7bb806c2636f9cd4b9b2d14040579f2847fceeccc8038","fit_origin":"imported","material_sha256":"32a90c12173f4081175608fb53707bccfef2783c24f9b74b50f08b109416a513","measurement_sha256":"8f66165b8f7e5bc51eec0b0e4fa036fc88e0ee439ed7dc9a22a2948227f64bc2","phases":["CIF012075","COD2310703","CIF001783"]},"material":{"declared_target":null,"declared_target_stoichiometry":null,"elements":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"elements of the declared precursors"},"value":["Bi","C","Li","Ni","O"]},"elements_basis":"declared","precursors":[{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Bi2O3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Li2CO3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"NiO"},"name":null,"purity":null,"target_amount":null}],"processing":[],"specimen":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture benchmark category"},"value":"Unheated physical mixture of the declared precursors."}},"measurement":{"instrument":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"instrument_export","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":".xrdml scan/header/source/instrumentControlSoftware"},"value":{"detector":"PIXcel1D-Medipix3 detector","geometry":null,"model":"AERIS","source_format":"harbor_packet","vendor":null}},"profile":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"instrument_registry","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"resolve_pattern_instrument_policy(measurement.instrument, 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/workspace/output/screen_output.txt","tool":"exec_command"},{"arguments_sha256":"9b4760b4e7995227fe14cb8fa514ff807ff8c7ef7bc3d75e98181a0fd79324b2","files":[],"index":9,"summary":"{\"max_output_tokens\":30000,\"session_id\":9845,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"9b4760b4e7995227fe14cb8fa514ff807ff8c7ef7bc3d75e98181a0fd79324b2","files":[],"index":10,"summary":"{\"max_output_tokens\":30000,\"session_id\":9845,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"9b4760b4e7995227fe14cb8fa514ff807ff8c7ef7bc3d75e98181a0fd79324b2","files":[],"index":11,"summary":"{\"max_output_tokens\":30000,\"session_id\":9845,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"9b4760b4e7995227fe14cb8fa514ff807ff8c7ef7bc3d75e98181a0fd79324b2","files":[],"index":12,"summary":"{\"max_output_tokens\":30000,\"session_id\":9845,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"600e76ac2a9312eb700c012a290a2568b9f9d1929b6424c418acbd1e9faf7f5b","files":[],"index":13,"summary":"head -5 /workspace/input/DEV006.xy && echo \"...\" && wc -l /workspace/input/DEV006.xy","tool":"exec_command"},{"arguments_sha256":"647a762b79950829f4edce500c0d4a06dd7da6d12ce666f634d83836c1055e15","files":[],"index":14,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\ndata = np.loadtxt('input/DEV006.xy')\nth = data[:,0]\nI = data[:,1]\n# Top 15 peaks\nidx = np.argsort(I)[-15:][::-1]\nfor i in idx:\n    print(f'{th[i]:.2f} deg  {I[i]:.0f}')\n\"","tool":"exec_command"},{"arguments_sha256":"b3948fe4bf15b7f2b34c1e985268e44b1917b336a731b9d0e593d25ed3ded5cf","files":[],"index":15,"summary":"cd /workspace && python3 physics/refine.py --case DEV006 --candidates CIF001779 CIF012075 COD2310703 --run-label precursors_3phase 2>&1 | tee /workspace/output/refine_precursors.txt","tool":"exec_command"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":16,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":17,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":18,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":19,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":20,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"abf2e44e4b3111c75d1bb2d380d7477a1476104b4aa3ad6a446e09010f8a212c","files":[],"index":21,"summary":"{\"max_output_tokens\":30000,\"session_id\":69492,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"640c4346f601bbb14de32457a3057dde69da0194fc9e345ccc54a880e02be8d8","files":[],"index":22,"summary":"cat /workspace/output/precursors_3phase/result.json","tool":"exec_command"},{"arguments_sha256":"098e32a8aa5123cb52fcf25268cd749a16cd9a18e982bdb3ddb05fb163d0a8cb","files":[],"index":23,"summary":"cd /workspace && python3 physics/screen.py --case DEV006 --residual precursors_3phase 2>&1 | tee /workspace/output/residual_check.txt","tool":"exec_command"},{"arguments_sha256":"f1b83eae34f98a0993af18394f802144583481b554c73e6afd96c15ac3d4d645","files":[],"index":24,"summary":"{\"max_output_tokens\":30000,\"session_id\":52147,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"ac2d10c8b93da95a68e28bb02d9876ace364485258ad6b38088d92db6dc2eef5","files":[],"index":25,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\ncsv = np.loadtxt('output/precursors_3phase/rietveld.csv', delimiter=',', skiprows=1)\nth = csv[:, 0]\nobs = csv[:, 1]\ncalc = csv[:, 2]\ndiff = csv[:, 3]\n\n# Find max residual regions\nI = np.abs(diff)\n# Top 20 residual points\nidx = np.argsort(I)[-20:][::-1]\nprint('Largest residuals (obs-calc):')\nfor i in idx:\n    print(f'  {th[i]:.2f} deg: diff={diff[i]:.0f}  obs={obs[i]:.0f}  calc={calc[i]:.0f}')\n\"","tool":"exec_command"},{"arguments_sha256":"c8ca15b8f0984f6ed915e6d0ea54696cea95ac73758e2057762877071188a42c","files":[],"index":26,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\n# Check what's at 52.5 deg in the data\ncsv = np.loadtxt('output/precursors_3phase/rietveld.csv', delimiter=',', skiprows=1)\nth = csv[:, 0]\nobs = csv[:, 1]\ndiff = csv[:, 3]\ncalc = csv[:, 2]\n\n# 52-53 deg region\nmask = (th > 52) & (th < 53.5)\nfor i in range(len(th)):\n    if mask[i]:\n        print(f'{th[i]:.4f} deg: obs={obs[i]:.0f} calc={calc[i]:.0f} diff={diff[i]:.0f}')\n\"","tool":"exec_command"},{"arguments_sha256":"a5ae3b9f7e2a8985b0fd2af8b63fe19ee146cec65eee9b3694ea917bdc068ecd","files":[],"index":27,"summary":"cd /workspace && python3 physics/refine.py --case DEV006 --candidates CIF001783 CIF012075 COD2310703 --run-label alt_bi2o3_3phase 2>&1 | tee /workspace/output/refine_alt_bi2o3.txt","tool":"exec_command"},{"arguments_sha256":"f09b5d5d33685fb2812994791d69d22c7998a0b54bb0c6d654b9b11b33810bba","files":[],"index":28,"summary":"{\"max_output_tokens\":30000,\"session_id\":43775,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"f09b5d5d33685fb2812994791d69d22c7998a0b54bb0c6d654b9b11b33810bba","files":[],"index":29,"summary":"{\"max_output_tokens\":30000,\"session_id\":43775,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"f09b5d5d33685fb2812994791d69d22c7998a0b54bb0c6d654b9b11b33810bba","files":[],"index":30,"summary":"{\"max_output_tokens\":30000,\"session_id\":43775,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"f09b5d5d33685fb2812994791d69d22c7998a0b54bb0c6d654b9b11b33810bba","files":[],"index":31,"summary":"{\"max_output_tokens\":30000,\"session_id\":43775,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"f09b5d5d33685fb2812994791d69d22c7998a0b54bb0c6d654b9b11b33810bba","files":[],"index":32,"summary":"{\"max_output_tokens\":30000,\"session_id\":43775,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"3a4e6f4ba566f482c8f441660744a52ff60fca5005c524ef130fe348cce61db4","files":[],"index":33,"summary":"cd /workspace && python3 -c \"\nimport numpy as np\ncsv = np.loadtxt('output/alt_bi2o3_3phase/rietveld.csv', delimiter=',', skiprows=1)\nth = csv[:, 0]\ndiff = csv[:, 3]\n# Top 15 residuals\nI = np.abs(diff)\nidx = np.argsort(I)[-15:][::-1]\nprint('Largest residuals (obs-calc) for CIF001783 fit:')\nfor i in idx:\n    print(f'  {th[i]:.2f} deg: diff={diff[i]:+.0f}')\n\"","tool":"exec_command"},{"arguments_sha256":"564e08ce060fcf925c2530060f5268301a617e1a5506218e2f0ed3d734dfec50","files":[],"index":34,"summary":"cd /workspace && python3 physics/screen.py --case DEV006 --residual alt_bi2o3_3phase 2>&1 | tee /workspace/output/residual_check2.txt","tool":"exec_command"},{"arguments_sha256":"990655ef2a7dfcc1a5354d3807d8f676d0d6d0b437e0684b0b89533630833dad","files":[],"index":35,"summary":"{\"max_output_tokens\":30000,\"session_id\":77836,\"yield_time_ms\":15000}","tool":"write_stdin"},{"arguments_sha256":"278fdbe451ab1b2b9bd0b93245608fe342f353100d268bdc4df9d156dbe2a9bc","files":[],"index":36,"summary":"cd /workspace && python3 -c \"\nimport json\nwith open('output/alt_bi2o3_3phase/result.json') as f:\n    r = json.load(f)\n\n# Final stage\nst = r['rietveld']\nprint('Final stage (rietveld):')\nprint(f'  Rwp={st[\\\"rwp\\\"]}%  Rexp={st[\\\"rexp\\\"]}%  GoF={st[\\\"gof\\\"]:.2f}')\nprint(f'  Rpb={st[\\\"rpb\\\"]}%  Rp={st[\\\"rp\\\"]}%')\nprint(f'  Converged: {st[\\\"converged\\\"]}')\nprint()\nfor p in st['phases']:\n    print(f'Phase: {p[\\\"phase_id\\\"]}')\n    wf = p['weight_fraction']\n    params = p['lattice_params']\n    initial = ","tool":"exec_command"},{"arguments_sha256":"676ca943e6d66a71943e2ab5f27a366cc00f1f2d90ce024bee0f96e5a25a5968","files":[],"index":37,"summary":"mkdir -p /workspace/output","tool":"exec_command"},{"arguments_sha256":"0c77b9aa5788f9a1f82b01e63cabb196cbcb08f784226cba29fb7ac599b1c31e","files":[],"index":38,"summary":"ls -la /workspace/output/ 2>/dev/null; echo \"---\"; ls -la /workspace/output/alt_bi2o3_3phase/ 2>/dev/null; echo \"---\"; ls -la /workspace/output/precursors_3phase/ 2>/dev/null; echo \"---\"; ls -la /workspace/output/*.txt 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"8536f8af956a2f7e03d431f08f2b30c8f5e0ce60ba281da45ee6475fec8f65ca","files":[],"index":39,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"690f90fbb01de8256137f3795c8b6a3216e630b9b8f55a125fce1b5e4be406dc","files":[],"index":40,"summary":"ls -la /workspace/output/ 2>/dev/null; echo \"===\"; ls -la /workspace/output/alt_bi2o3_3phase/ 2>/dev/null; echo \"===\"; ls -la /workspace/output/precursors_3phase/ 2>/dev/null; echo \"===\"; ls -la /workspace/output/*.txt 2>/dev/null","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":41,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"72f832a4505465cf43f1f762daf6b4c5d1d55ea0df8829aa73210b8c15b76681","files":[],"index":42,"summary":"cat /workspace/output/alt_bi2o3_3phase/result.json","tool":"exec_command"},{"arguments_sha256":"0684b712e2afb0b26153d6dc7b117d38cdc143a8f8206d16ecc20e98040ccbb4","files":[],"index":43,"summary":"cat /workspace/output/precursors_3phase/result.json","tool":"exec_command"},{"arguments_sha256":"a5a45015e5e427bbae3605aafed7c6011b24f081b27931caebb2358c78fc4756","files":[],"index":44,"summary":"cat /workspace/output/screen_output.txt","tool":"exec_command"},{"arguments_sha256":"0884c482c19e6027527bcf1cf17807912430d94bae210c48c79379963140937f","files":[],"index":45,"summary":"cat /workspace/output/residual_check2.txt","tool":"exec_command"},{"arguments_sha256":"c3fde5d0a14346aedb3e86e6b75d09b3e5cfb642f9183711092a4825ad208bca","files":[],"index":46,"summary":"cat /workspace/output/refine_alt_bi2o3.txt","tool":"exec_command"},{"arguments_sha256":"ffbd92618e2d90e1cff5e71d6f12561968173594c452ea063a70e69901ea4607","files":[],"index":47,"summary":"python3 /workspace/physics/case_brief.py --case DEV006 2>&1","tool":"exec_command"},{"arguments_sha256":"4252feba48c2e9ff07e15db5092ba5a06cb79260d27500a93a4738dc5e86c068","files":[],"index":48,"summary":"python3 /workspace/physics/candidates.py --case DEV006 2>&1 | head -30","tool":"exec_command"},{"arguments_sha256":"38ae764248bfc5a553d1c59f00e5f7a0a918d7fe500375d340af326d113715ed","files":[],"index":49,"summary":"{\"chars\":\"\",\"session_id\":32676,\"yield_time_ms\":15000}","tool":"write_stdin"},{"arguments_sha256":"7f4c47d2c2fcc1446ac298049895524a6dd097a585dabe1a846969f1acf128a5","files":[],"index":50,"summary":"cat /workspace/output/residual_check.txt","tool":"exec_command"},{"arguments_sha256":"50bbba684725a125e733106e2c02716b91b03f50968da62f8c4562971e7561ae","files":[],"index":51,"summary":"python3 << 'PYEOF'\nimport csv, math\n\n# Read the rietveld.csv for alt_bi2o3_3phase\ndata = []\nwith open('/workspace/output/alt_bi2o3_3phase/rietveld.csv') as f:\n    reader = csv.DictReader(f)\n    for row in reader:\n        data.append({\n            'two_theta': float(row['two_theta']),\n            'observed': float(row['observed']),\n            'calculated': float(row['calculated']),\n            'difference': float(row['difference'])\n        })\n\n# Calculate Rwp, Rp independently\nss_w = 0.0  # weig","tool":"exec_command"},{"arguments_sha256":"5608fe90757141eed980f88a1f17a871b57513eb04c1deb0d0c5f68c2ce2b525","files":[],"index":52,"summary":"cat > /workspace/output/analysis.json << 'JSONEOF'\n{\n  \"case_id\": \"DEV006\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF001783\",\n      \"formula\": \"Bi2O3\",\n      \"space_group\": \"P2_1/c (No. 14)\",\n      \"crystal_system\": \"monoclinic\",\n      \"evidence\": \"Screen ranking #2 of 60 candidates (fom 0.71, cov 0.90, 0 missed lines). Phase search hypothesis H1 included this formula. Rietveld refinement converged with Rwp 3.54%. Refined cell shifts all under 0.2%: a +0.11%, b +0.17%, c +0.14%, beta +0.01%","tool":"exec_command"},{"arguments_sha256":"f7127d3746e44377bae2f6fb388fd056e586bf4c88923be06635417c802408ae","files":[],"index":53,"summary":"python3 -c \"import json; d=json.load(open('/workspace/output/analysis.json')); print('Valid JSON'); print(f'Phases: {len(d[\\\"phases\\\"])}'); print(f'Weight fractions: {d[\\\"weight_fractions\\\"]}'); print(f'Sum: {sum(d[\\\"weight_fractions\\\"].values()):.4f}'); print(f'Artifacts: {len(d[\\\"fit_artifacts\\\"])} files'); print(f'Limitations: {len(d[\\\"limitations\\\"])} items')\"","tool":"exec_command"}],"wall_seconds":932.650197},"status":"completed"},"parent":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","rationale":"","root":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"4b131ee352ac4ade3164e2fa86f94965b8a23dc991eee6c79ff19c6b2b34d2c1","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"362892a3f7cf00d83851ae0df1fa9f09366cfcce5d1f3368d07b2b511840e385","size_bytes":832663,"stage":"rietveld"},"gof":1.8247422680412373,"phases":[{"candidate_id":"CIF001783","cell":{"a":5.85107,"alpha":90.0,"b":8.17145,"beta":112.979,"c":7.5137,"gamma":90.0},"spacegroup_no":14,"weight_percent":22.27417892685531,"weight_percent_error":0.43},{"candidate_id":"CIF012075","cell":{"a":4.178585,"alpha":90.0,"b":4.178585,"beta":90.0,"c":4.178585,"gamma":90.0},"spacegroup_no":225,"weight_percent":37.90833530386089,"weight_percent_error":0.73},{"candidate_id":"COD2310703","cell":{"a":8.4243,"alpha":90.0,"b":4.97614,"beta":115.42,"c":6.23316,"gamma":90.0},"spacegroup_no":15,"weight_percent":39.8174857692838,"weight_percent_error":1.1}],"quantification":"restricted_profile","rwp_percent":3.54,"stage":"rietveld"},"fit_basis":"4b131ee352ac4ade3164e2fa86f94965b8a23dc991eee6c79ff19c6b2b34d2c1","fit_origin":"imported","material_sha256":"32a90c12173f4081175608fb53707bccfef2783c24f9b74b50f08b109416a513","measurement_sha256":"8f66165b8f7e5bc51eec0b0e4fa036fc88e0ee439ed7dc9a22a2948227f64bc2","phases":["CIF001783","CIF012075","COD2310703"]},"material":{"declared_target":null,"declared_target_stoichiometry":null,"elements":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"elements of the declared precursors"},"value":["Bi","C","Li","Ni","O"]},"elements_basis":"declared","precursors":[{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Bi2O3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Li2CO3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"NiO"},"name":null,"purity":null,"target_amount":null}],"processing":[],"specimen":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture benchmark category"},"value":"Unheated physical mixture of the declared 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/workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"36c27742b3f42798786a6a8bd82753705a00b746a88a9d31f62065e33af4a58a","files":[],"index":1,"summary":"python3 /workspace/physics/case_brief.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"34fa89688ff74e333e96b846c692b2210b494ab03379a357039a7123890a6e26","files":[],"index":2,"summary":"python3 /workspace/physics/candidates.py --case DEV006","tool":"exec_command"},{"arguments_sha256":"3bcc382aba163f2014b7a105aebac710e3ba123387957390dd7f3c393052d82b","files":[],"index":3,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":39545,\"yield_time_ms\":15000}","tool":"write_stdin"},{"arguments_sha256":"6a492f52ec06e44d6f98e9439e5924d785f4a8a2214c5d5a19bf62e6d6d2a2ea","files":[],"index":4,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV006 2>&1","tool":"exec_command"},{"arguments_sha256":"eaf33db7ce0e40a02db868e59cba4158640fe7a94cd8fa5ba2228b4e735cceb0","files":[],"index":5,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":29983,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"eaf33db7ce0e40a02db868e59cba4158640fe7a94cd8fa5ba2228b4e735cceb0","files":[],"index":6,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":29983,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"e0c5d6a049248598db4bdd6361772e7762134dea77a1b86d6d50779b4156eea9","files":[],"index":7,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012075 CIF001779 COD2310703 --run-label run1_precursors 2>&1","tool":"exec_command"},{"arguments_sha256":"0bf997bdd90ae22fd597288e5ce9f445da06bafda56933e39a8379b52eecad7c","files":[],"index":8,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":73969,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"0bf997bdd90ae22fd597288e5ce9f445da06bafda56933e39a8379b52eecad7c","files":[],"index":9,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":73969,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"0bf997bdd90ae22fd597288e5ce9f445da06bafda56933e39a8379b52eecad7c","files":[],"index":10,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":73969,\"yield_time_ms\":60000}","tool":"write_stdin"},{"arguments_sha256":"0a5c6edcbedd690b919a23c299508592a642d909ef6d56236a933be0d948b03f","files":[],"index":11,"summary":"cat /workspace/output/run1_precursors/result.json","tool":"exec_command"},{"arguments_sha256":"cbd4ee09f5aa517cf8f6b40a8dfeeab0786c5c4116eb671495fc074a42609ba7","files":[],"index":12,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --residual run1_precursors 2>&1","tool":"exec_command"},{"arguments_sha256":"b51c70fac6588f42fad1cf7c60659b0f3b64fd98331a441a8a279bfe80ff9598","files":[],"index":13,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV006 --residual run1_precursors 2>&1","tool":"exec_command"},{"arguments_sha256":"353cccc91a2032d8880d6257bd2f9c62c1a4a3133525b7c125bce37ae780d281","files":[],"index":14,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":61672,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"95224b11c1b396ee3143b54beb09eebe1bed9700a0947fef90a87e8d38a6ef51","files":[],"index":15,"summary":"cat /workspace/input/manifest.json | python3 -c \"import json,sys; d=json.load(sys.stdin); print(json.dumps(d, indent=2))\"","tool":"exec_command"},{"arguments_sha256":"448a327212d231a1a61a05f969e39006653471295d0b141c5eda6244aa6342b8","files":[],"index":16,"summary":"python3 -c \"\nimport csv\n# Read the rietveld difference curve\nwith open('/workspace/output/run1_precursors/rietveld.csv') as f:\n    reader = csv.reader(f)\n    header = next(reader)\n    print('Header:', header)\n    rows = list(reader)\n\nn = len(rows)\ntwo_theta = [float(r[0]) for r in rows]\nobserved = [float(r[1]) for r in rows]\ncalc = [float(r[2]) for r in rows]\ndiff = [float(r[3]) for r in rows]\n\nmax_obs = max(observed)\nmax_diff = max(abs(d) for d in diff)\nmean_diff = sum(d for d in diff) / n\nrms_","tool":"exec_command"},{"arguments_sha256":"27000b46d3a462ac16ebd7c6cf2bed18f771ac1ecab79800d38d83a23319f3c6","files":[],"index":17,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012075 CIF001783 COD2310703 --run-label run2_Bi2O3alt 2>&1","tool":"exec_command"},{"arguments_sha256":"2f54dfe5b85dc30e2af23946065201f57e55f4428ceffa1475b50ea4ef7c6117","files":[],"index":18,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":89384,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"2f54dfe5b85dc30e2af23946065201f57e55f4428ceffa1475b50ea4ef7c6117","files":[],"index":19,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":89384,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"9757d413d91a671fd7c8e1603b50561fe655e82ae3908404838086e48af5a0f0","files":[],"index":20,"summary":"cd /workspace && timeout 900 python3 /workspace/physics/screen.py --case DEV006 --residual run2_Bi2O3alt 2>&1","tool":"exec_command"},{"arguments_sha256":"d9926f9d29807c64627723862a17855590fa5dfd033ed5bea5b6c6252ecca440","files":[],"index":21,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":58258,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"18f638fd3f9edc5e5e442c1c870117dbd1fff83e0e50809af70ca11cf90ecab4","files":[],"index":22,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012075 CIF001783 CIF008546 --run-label run3_Li2CO3alt 2>&1","tool":"exec_command"},{"arguments_sha256":"53325dc5601b6bfcb69421c7e0291441f3ab5094dbb285b71c832c4849e85c22","files":[],"index":23,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":7306,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"fefe4a9f0699ceb0c549058b5862388563313e0bc7407928c0412bdb11cc9422","files":[],"index":24,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012076 CIF001783 COD2310703 --run-label run4_NiOalt1 2>&1","tool":"exec_command"},{"arguments_sha256":"2ed52d10f5266dc1851e8db3a1d9152c88e12a7a7455d78216dfd893d81de1b8","files":[],"index":25,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":10341,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"2ed52d10f5266dc1851e8db3a1d9152c88e12a7a7455d78216dfd893d81de1b8","files":[],"index":26,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":10341,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"e6beb6a558ef85daf0a9d1a3c7fa25f94d6273492c6d9092ef259e169cb45e8f","files":[],"index":27,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012077 CIF001783 COD2310703 --run-label run5_NiOalt2 2>&1","tool":"exec_command"},{"arguments_sha256":"567af5bb97b32335323f13a66120ca4f9f85a1dec2c663a18b6000959c503859","files":[],"index":28,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":16114,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"567af5bb97b32335323f13a66120ca4f9f85a1dec2c663a18b6000959c503859","files":[],"index":29,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":16114,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"15c75566454b2afa3714e3e35189aaea0ae6994f7712a89be294ab7fa123acd5","files":[],"index":30,"summary":"cd /workspace && timeout 3600 python3 /workspace/physics/refine.py --case DEV006 --candidates CIF012078 CIF001783 COD2310703 --run-label run6_NiO_R3m 2>&1","tool":"exec_command"},{"arguments_sha256":"bb568cd0a3ed3806f23b7c0251aec766580fa4e5590ebaadcc2c72ae93add197","files":[],"index":31,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":7936,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"bb568cd0a3ed3806f23b7c0251aec766580fa4e5590ebaadcc2c72ae93add197","files":[],"index":32,"summary":"{\"chars\":\"\",\"max_output_tokens\":10000,\"session_id\":7936,\"yield_time_ms\":120000}","tool":"write_stdin"},{"arguments_sha256":"382565fe446bdbe781a8bb103b5bee7f79fa77631bc8ca7ed1f46a5d70a7669f","files":[],"index":33,"summary":"cat /workspace/output/run4_NiOalt1/result.json | python3 -c \"\nimport json,sys\nd=json.load(sys.stdin)\nr=d['rietveld']\nfor p in r['phases']:\n    wf = p['weight_fraction']\n    wfe = p.get('weight_fraction_error', 'N/A')\n    lp = p['lattice_params']\n    lp0 = p['lattice_params_initial']\n    print(f\\\"{p['phase_id']}: wt%={wf:.2f}, err={wfe}, cell={lp}, init={lp0}\\\")\nprint(f\\\"Rwp={r['rwp']}, Rexp={r['rexp']}, GoF={r['gof']:.4f}\\\")\nprint(f\\\"Converged={r['converged']}\\\")\nprint(f\\\"Iterations={r['iteratio","tool":"exec_command"},{"arguments_sha256":"6744aa431823173eae6fa9397eb662d0b444ff414bf174773cae361170da0b68","files":[],"index":34,"summary":"mkdir -p /workspace/output","tool":"exec_command"},{"arguments_sha256":"8393fd0bdd4ddf8393255eb015d8b91b887eb0ac65ff23761a9fa1ca7e2b0ac2","files":[],"index":35,"summary":"cat > /workspace/output/analysis.json << 'ANALYSIS_EOF'\n{\n  \"case_id\": \"DEV006\",\n  \"phases\": [\n    {\n      \"candidate_id\": \"CIF012076\",\n      \"formula\": \"NiO\",\n      \"space_group\": \"Fm-3m (225)\",\n      \"evidence\": [\n        \"Unheated physical mixture precursor (NiO declared)\",\n        \"Screening rank 5 (tied top for NiO): fom=0.44, cov=1.00, expl=20%, missed=0/3\",\n        \"Refined cell a=4.1786 (shift -0.03% from CIF a=4.180), smallest cell shift among NiO candidates\",\n        \"Fm-3m space group","tool":"exec_command"},{"arguments_sha256":"e76fe3ead121f32c556fc8c070c2a0908b129e362a6bc786be1d52c2f4558eb2","files":[],"index":36,"summary":"python3 -c \"import json; d=json.load(open('/workspace/output/analysis.json')); print('Valid JSON'); print(f'Phases: {len(d[\\\"phases\\\"])}'); print(f'Weight fractions: {d[\\\"weight_fractions\\\"]}'); print(f'Sum: {sum(d[\\\"weight_fractions\\\"].values()):.4f}'); print(f'Fit statistics keys: {list(d[\\\"fit_statistics\\\"].keys())}')\"","tool":"exec_command"},{"arguments_sha256":"1d047f9e3c89e36b4572895987ac361dff3cf4a0ea482c88400885fe4577b541","files":[],"index":37,"summary":"echo \"=== Output directory contents ===\" && find /workspace/output -type f | sort && echo \"=== File sizes ===\" && du -sh /workspace/output/* 2>/dev/null && echo \"=== analysis.json top-level keys ===\" && python3 -c \"import json; d=json.load(open('/workspace/output/analysis.json')); [print(f'  {k}') for k in d.keys()]\"","tool":"exec_command"},{"arguments_sha256":"c11a466cbdd11094d72b1f9b89170e28770f106ac0b0c48c92c68ee00da8040f","files":[],"index":38,"summary":"ls -la /workspace/output/","tool":"exec_command"},{"arguments_sha256":"68790b602e965bba7abcc1c6a5fb2baf8c23604852bca2f0b7cb33fcdc9bf51a","files":[],"index":39,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"922bff281ed54d98465245d003bd237f044ba938f51f460f691978a8c738ce33","files":[],"index":40,"summary":"cat /workspace/output/run4_NiOalt1/result.json","tool":"exec_command"},{"arguments_sha256":"25773a20e282337cff59706dd56c07d37b333898a97972480ba2c906e1d5f67e","files":[],"index":41,"summary":"find /workspace/output/run4_NiOalt1/ -name \"*.log\" -o -name \"*.txt\" -o -name \"*.csv\" | head -20","tool":"exec_command"},{"arguments_sha256":"7b4f78d8f0dcb694fca4d8864ef71f8cfdc1a3d21ea4baf656d213e936f4f6fd","files":[],"index":42,"summary":"ls -la /workspace/output/run4_NiOalt1/fit/ 2>/dev/null; find /workspace/output/run4_NiOalt1/ -type f | sort","tool":"exec_command"},{"arguments_sha256":"06afa8c4027fd8d1d7b711c95165b6f1c5040a1c5e9c096f9f0bc9d9cbd28973","files":[],"index":43,"summary":"cat /workspace/output/run4_NiOalt1/fit/DEV006_rietveld.lst","tool":"exec_command"},{"arguments_sha256":"153180aef0773992f453440a1cda0f3ca82adc74f9635ec9381aa98cd8da5d4b","files":[],"index":44,"summary":"for run in run1_precursors run2_Bi2O3alt run3_Li2CO3alt run5_NiOalt2 run6_NiO_R3m; do echo \"=== $run ===\"; python3 -c \"import json; d=json.load(open('/workspace/output/$run/result.json')); print('Rwp:', d['rietveld']['rwp'], 'GoF:', d['rietveld']['gof']); [print(f\\\"  {p['phase_id']}: {p['weight_fraction']:.2f}%\\\") for p in d['rietveld']['phases']]\"; done","tool":"exec_command"},{"arguments_sha256":"7ef8ff676b2d908c911cb37aabb9f08be42ef64b4bb6ea68d05acc111c99828c","files":[],"index":45,"summary":"python3 -c \"\nimport json\nd = json.load(open('/workspace/output/run4_NiOalt1/result.json'))\nfor stage in ['pawley', 'rietveld_lattice', 'rietveld_profile', 'rietveld']:\n    s = d[stage]\n    print(f'=== {stage} ===')\n    print(f'  Rwp={s[\\\"rwp\\\"]}, Rp={s[\\\"rp\\\"]}, Rpb={s[\\\"rpb\\\"]}, Rexp={s[\\\"rexp\\\"]}, GoF={s[\\\"gof\\\"]:.2f}')\n    print(f'  rho={s[\\\"rho\\\"]}, dw={s[\\\"durbin_watson\\\"]}, iterations={s[\\\"iteration_count\\\"]}')\n\"","tool":"exec_command"},{"arguments_sha256":"9fb215d6fc6edfe6d0ccd6c0b997a04f5d04b76e6be82e430303690ecfc85aa6","files":[],"index":46,"summary":"cat /workspace/physics/README.md","tool":"exec_command"},{"arguments_sha256":"4bdae87ef039ee84b5cb644348959ee02a9b4615c6fa04a9ce30330d67b5baf4","files":[],"index":47,"summary":"cat /workspace/input/manifest.json","tool":"exec_command"},{"arguments_sha256":"3304942063a84f072ec9ce7dd453e1687cea3d12e60aa8c41dfb7520145abbe7","files":[],"index":48,"summary":"python3 /workspace/physics/screen.py --case DEV006 --no-search 2>&1 | head -80","tool":"exec_command"},{"arguments_sha256":"affbac62afa8b8328249ff4fa04a34f66adb71ecde81a3c9897764eb6eb19b14","files":[],"index":49,"summary":"{\"chars\":\"\",\"session_id\":35333,\"yield_time_ms\":30000}","tool":"write_stdin"},{"arguments_sha256":"940f84fdd03e4a42af30b33f8bc26b30f84f20053b8426f0c250d67930f0b4b7","files":[],"index":50,"summary":"python3 /workspace/physics/screen.py --case DEV006 --residual run4_NiOalt1 2>&1","tool":"exec_command"},{"arguments_sha256":"008c0c6fb455ba31fc3ebb41559f3495812cbd52f8d01782ef459b05b8787283","files":[],"index":51,"summary":"{\"chars\":\"\",\"session_id\":35392,\"yield_time_ms\":15000}","tool":"write_stdin"},{"arguments_sha256":"a5a40393bea645f9df402fe72b37604c53833edb08778da9040239f1c560455a","files":[],"index":52,"summary":"python3 << 'PYEOF'\nimport json\n\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\n\n# Fix pawley iterations: was 110, actual 83\nd['fit_statistics']['pawley']['iterations'] = 83\n\n# Fix rietveld stage stats\nd['fit_statistics']['rietveld']['R_p']['value'] = 2.76\nd['fit_statistics']['rietveld']['R_pb']['value'] = 14.61\nd['fit_statistics']['rietveld']['rho'] = 1.25\nd['fit_statistics']['rietveld']['durbin_watson'] = 0.65\n\n# Fix stage_degradation delta (use actual values)\nd['fit_st","tool":"exec_command"},{"arguments_sha256":"fde61bea71075bcf209efd6b9b3108481b9ded72a16117c7ebdfd328225aaf0a","files":[],"index":53,"summary":"python3 -c \"\nimport json\nwith open('/workspace/output/analysis.json') as f:\n    d = json.load(f)\n\nprint('=== Verification ===')\nprint('Pawley iterations:', d['fit_statistics']['pawley']['iterations'])\nprint('Rietveld Rp:', d['fit_statistics']['rietveld']['R_p']['value'])\nprint('Rietveld Rpb:', d['fit_statistics']['rietveld']['R_pb']['value'])\nprint('Rietveld rho:', d['fit_statistics']['rietveld']['rho'])\nprint('Rietveld DW:', d['fit_statistics']['rietveld']['durbin_watson'])\nprint('Weight fracti","tool":"exec_command"},{"arguments_sha256":"68790b602e965bba7abcc1c6a5fb2baf8c23604852bca2f0b7cb33fcdc9bf51a","files":[],"index":54,"summary":"cat /workspace/output/analysis.json","tool":"exec_command"},{"arguments_sha256":"1c13b35ca25a78abaa8498c36d0c3fe222815c7dc20174517589b113954e68eb","files":[],"index":55,"summary":"python3 -c \"\nimport json, os\nd = json.load(open('/workspace/output/analysis.json'))\nfor path in d['fit_artifacts']:\n    exists = os.path.exists(path)\n    status = 'OK' if exists else 'MISSING'\n    print(f'{status}: {path}')\n\"","tool":"exec_command"},{"arguments_sha256":"ef9c6e91e15c8482d901b33387308812cb3aa907019ca19d70704b0e5cf0e271","files":[],"index":56,"summary":"python3 -c \"import json; json.load(open('/workspace/output/analysis.json')); print('Valid JSON'); import os; print(f'Size: {os.path.getsize(\\\"/workspace/output/analysis.json\\\")} bytes')\" && ls -la /workspace/output/","tool":"exec_command"}],"wall_seconds":1541.178048},"status":"completed"},"parent":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","rationale":"","root":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61","schema_version":"axa.attempt.v3","tool":{"axa_git_sha":"1c387a56923bdacecda043c4edf6a198305f2129","backend":null,"name":"harbor_importer","version":"1"}},"digest":"e25efb84e5c3d17030bbe13e28c98c3827d6e1e83f04b44ebe95c1da9cc2ef62","state_after":{"hypothesis":{"fit":{"curve":{"media_type":"text/csv","role":"fit_curve","sha256":"1632f5eb771e3c6bdf5e105bc59768b72f5c33363848d546e2a67e2a8fc2acf0","size_bytes":832659,"stage":"rietveld"},"gof":1.8247422680412373,"phases":[{"candidate_id":"CIF012076","cell":{"a":4.178586,"alpha":90.0,"b":4.178586,"beta":90.0,"c":4.178586,"gamma":90.0},"spacegroup_no":225,"weight_percent":37.852061326548636,"weight_percent_error":0.74},{"candidate_id":"CIF001783","cell":{"a":5.85107,"alpha":90.0,"b":8.17145,"beta":112.979,"c":7.5137,"gamma":90.0},"spacegroup_no":14,"weight_percent":22.239845005516756,"weight_percent_error":0.43},{"candidate_id":"COD2310703","cell":{"a":8.424199999999999,"alpha":90.0,"b":4.97614,"beta":115.42,"c":6.23317,"gamma":90.0},"spacegroup_no":15,"weight_percent":39.9080936679346,"weight_percent_error":1.2}],"quantification":"restricted_profile","rwp_percent":3.54,"stage":"rietveld"},"fit_basis":"e25efb84e5c3d17030bbe13e28c98c3827d6e1e83f04b44ebe95c1da9cc2ef62","fit_origin":"imported","material_sha256":"32a90c12173f4081175608fb53707bccfef2783c24f9b74b50f08b109416a513","measurement_sha256":"8f66165b8f7e5bc51eec0b0e4fa036fc88e0ee439ed7dc9a22a2948227f64bc2","phases":["CIF012076","CIF001783","COD2310703"]},"material":{"declared_target":null,"declared_target_stoichiometry":null,"elements":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"elements of the declared precursors"},"value":["Bi","C","Li","Ni","O"]},"elements_basis":"declared","precursors":[{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Bi2O3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"Li2CO3"},"name":null,"purity":null,"target_amount":null},{"amount":null,"cas_number":null,"formula":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture file name, precursor tokens only (amount tokens withheld)"},"value":"NiO"},"name":null,"purity":null,"target_amount":null}],"processing":[],"specimen":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"synthesis_recipe","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"DARA precursor_mixture benchmark category"},"value":"Unheated physical mixture of the declared precursors."}},"measurement":{"instrument":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"instrument_export","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":".xrdml scan/header/source/instrumentControlSoftware"},"value":{"detector":"PIXcel1D-Medipix3 detector","geometry":null,"model":"AERIS","source_format":"harbor_packet","vendor":null}},"profile":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"instrument_registry","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":"resolve_pattern_instrument_policy(measurement.instrument, measurement.detector)"},"value":{"instrument_profile":"Aeris-fds-Pixcel1d-Medipix3","reason_codes":["instrument_profile_proxy"],"resolver_confidence":"inferred"}},"radiation":{"source":{"adapter":{"adapter_id":"harbor_packet","version":"1"},"channel":"instrument_export","document":"a7f3f20ea39a439bf5635270b6d15fb5c2ce65dabba6cdae78443a4acf1cf6bb","kind":"document","locator":".xrdml usedWavelength/kAlpha1"},"value":{"anode":"Cu","kind":"tube"}},"two_theta_deg":[10.00943322,99.99442286],"wavelength_provenance":null},"root":"d51a3823f766972d0fab8d133e6485b00f181d5e857456b37965ada8c8899c61"}}],"task_kind":"confirmation"}