refactor: regenerate baselines for the loader API refactor (q2mm#281 companion)

benchmarks/ch3f/convergence/paper_metrics.json

@@ -1,13 +1,16 @@
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-    "timestamp_utc": "2026-05-24T19:48:10.089779+00:00",
-    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /tmp/regen-test --combined-output /tmp/regen-test/baseline_all.json",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
     "q2mm": {
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+      "git_sha": "1efff97bb11fd6c2c4b7db8a0841ee05384a1151",
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@@ -26,11 +29,11 @@
     "seminario": {
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   }

benchmarks/ch3f/convergence/validation_results.json

@@ -1,13 +1,16 @@
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-    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /tmp/regen-test --combined-output /tmp/regen-test/baseline_all.json",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
     "q2mm": {
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+      "git_sha": "1efff97bb11fd6c2c4b7db8a0841ee05384a1151",
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@@ -26,17 +29,17 @@
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     "ratio_status": "ok",
     "ratio_passes": true,
     "seminario": {
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+        "r2": 0.9503878113616433,
+        "rmsd": 191.3684928169649,
+        "mae": 176.68442571266712
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     "skipped": true,

benchmarks/heck-relay/convergence/paper_metrics.json

@@ -1,15 +1,15 @@
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-    "command_line": "scripts/regenerate_convergence_results.py --system heck-relay --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
     "q2mm": {
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+      "git_sha": "1efff97bb11fd6c2c4b7db8a0841ee05384a1151",
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     "q2mm_data": {
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@@ -29,23 +29,23 @@
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+      "_objective_score": 3400409.485135087,
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benchmarks/heck-relay/convergence/validation_results.json

@@ -1,15 +1,15 @@
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-    "command_line": "scripts/regenerate_convergence_results.py --system heck-relay --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
     "q2mm": {
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     "q2mm_data": {
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+      "git_sha": "a7465fb2536997f53d1e5a4e9712693677572bcb",
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     "maxiter": 500,
@@ -29,23 +29,23 @@
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-    "initial_obj_score": 3463632.4167105975,
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+    "initial_obj_score": 3400409.485135087,
+    "initial_jaxloss": 4434648.082002647,
+    "ratio": 1.3041511916105226,
     "ratio_status": "out_of_band",
     "ratio_passes": false,
     "seminario": {
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+        "rmsd": 0.045942018934896287,
+        "mae": 0.026538756059945573
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+        "mae": 5.226622810339419
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benchmarks/pd-1,4-conjugate-addition/convergence/paper_metrics.json

@@ -1,13 +1,16 @@
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-    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /tmp/regen-test --combined-output /tmp/regen-test/baseline_all.json",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
     "q2mm": {
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@@ -26,23 +29,23 @@
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benchmarks/pd-1,4-conjugate-addition/convergence/validation_results.json

@@ -1,13 +1,16 @@
 {
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-    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /tmp/regen-test --combined-output /tmp/regen-test/baseline_all.json",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
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@@ -26,29 +29,29 @@
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     "skipped": true,

benchmarks/pd-allyl-amination/convergence/paper_metrics.json

@@ -1,19 +1,19 @@
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-    "command_line": "scripts/regenerate_convergence_results.py --system rh-enamide --system pd-allyl --output-dir /home/eric/repos/q2mm-data/benchmarks",
+    "timestamp_utc": "2026-05-25T14:55:17.583903+00:00",
+    "command_line": "scripts/regenerate_convergence_results.py --skip-optimization --output-dir /home/eric/repos/q2mm-data/benchmarks --combined-output /tmp/regen-all-baseline.json",
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@@ -29,45 +29,23 @@
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