diff --git a/benchmarks/ch3f/convergence/ch3f_optimized.fld b/benchmarks/ch3f/convergence/ch3f_optimized.fld index 38d69b5..302c639 100644 --- a/benchmarks/ch3f/convergence/ch3f_optimized.fld +++ b/benchmarks/ch3f/convergence/ch3f_optimized.fld @@ -1,7 +1,7 @@ C OPT OPT Generated 9 AUTO - 1 C1 F1 3.0000 4.2052 + 1 C1 F1 3.0000 4.2074 1 C1 H1 0.9640 5.3243 - 2 F1 C1 H1 109.8505 0.2417 - 2 H1 C1 H2 104.6142 0.2956 + 2 F1 C1 H1 109.8571 0.2418 + 2 H1 C1 H2 104.5960 0.2956 -3 diff --git a/benchmarks/ch3f/convergence/paper_metrics.json b/benchmarks/ch3f/convergence/paper_metrics.json index ae32d1c..11140de 100644 --- a/benchmarks/ch3f/convergence/paper_metrics.json +++ b/benchmarks/ch3f/convergence/paper_metrics.json @@ -1,18 +1,16 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-26T22:46:05.442842+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system ch3f --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T06:49:30.263446+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system ch3f --n-evals 5 --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "85dc8c98957b7aee8ee29116da24a36c88817447", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "8b0fcb7942146e7fdecd756852657f7dad98013b", - "git_dirty": false + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", + "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, + "n_evals": 5, "skip_optimization": false, "devices": { "jax_devices": [ @@ -29,21 +27,21 @@ "seminario": { "frequency": { "n_refs": 9, - "r2": 0.9503878113616431, - "rmsd": 191.36849281696536, - "mae": 176.68442571266718 + "r2": 0.950387811361643, + "rmsd": 191.3684928169656, + "mae": 176.6844257126675 }, - "_objective_score": 0.3295971003873329, + "_objective_score": 0.32959710038733253, "_total_refs": 9 }, "optimized": { "frequency": { "n_refs": 9, - "r2": 0.9999174594677313, - "rmsd": 7.8056644135184685, - "mae": 4.711071817934049 + "r2": 0.9999175143722802, + "rmsd": 7.803067884489719, + "mae": 4.711706981011149 }, - "_objective_score": 0.0005483555724282448, + "_objective_score": 0.0005479908156895794, "_total_refs": 9 } } diff --git a/benchmarks/ch3f/convergence/validation_results.json b/benchmarks/ch3f/convergence/validation_results.json index f80081c..a41096d 100644 --- a/benchmarks/ch3f/convergence/validation_results.json +++ b/benchmarks/ch3f/convergence/validation_results.json @@ -1,18 +1,16 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-26T22:46:05.442842+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system ch3f --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T06:49:30.263446+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system ch3f --n-evals 5 --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "85dc8c98957b7aee8ee29116da24a36c88817447", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "8b0fcb7942146e7fdecd756852657f7dad98013b", - "git_dirty": false + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", + "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, + "n_evals": 5, "skip_optimization": false, "devices": { "jax_devices": [ @@ -29,33 +27,42 @@ "system": "ch3f", "n_molecules": 1, "n_active_params": 8, - "initial_obj_score": 0.3295971003873329, - "initial_jaxloss": 0.329597100387326, - "ratio": 0.9999999999999789, + "initial_obj_score": 0.32959710038733253, + "initial_jaxloss": 0.3295971003873276, + "ratio": 0.999999999999985, "ratio_status": "ok", "ratio_passes": true, "seminario": { "frequency": { "n_refs": 9, - "r2": 0.9503878113616431, - "rmsd": 191.36849281696536, - "mae": 176.68442571266718 + "r2": 0.950387811361643, + "rmsd": 191.3684928169656, + "mae": 176.6844257126675 } }, - "final_obj_score": 0.0005483555724282448, - "improvement_pct": 99.83362852046216, - "n_iterations": 92, + "final_obj_score": 0.0005479908156895794, + "initial_obj_score_mean": 0.3295971003873337, + "initial_obj_score_ci95": 1.2927107972269404e-15, + "final_obj_score_mean": 0.0005479908156895802, + "final_obj_score_ci95": 3.5906352705735415e-17, + "improvement_pct_mean": 99.83373918792198, + "improvement_significant": true, + "final_optimizer_score": 0.0005479908156895699, + "initial_optimizer_score": 0.32959710038733275, + "n_iterations": 100, "n_evaluations": 2, "converged": true, - "message": "CONVERGENCE: NORM OF PROJECTED GRADIENT <= PGTOL", + "message": "CONVERGENCE: RELATIVE REDUCTION OF F <= FACTR*EPSMCH", "jac_mode": "jax_loss", - "opt_time_s": 3.2913138029980473, + "opt_time_s": 2.3429676729720086, + "improvement_pct": 99.83373918792198, + "surrogate_improvement_pct": 99.83373918792199, "optimized": { "frequency": { "n_refs": 9, - "r2": 0.9999174594677313, - "rmsd": 7.8056644135184685, - "mae": 4.711071817934049 + "r2": 0.9999175143722802, + "rmsd": 7.803067884489719, + "mae": 4.711706981011149 } } } diff --git a/benchmarks/heck-relay/convergence/heck-relay_optimized.fld b/benchmarks/heck-relay/convergence/heck-relay_optimized.fld index 5aa3e01..a6c51a7 100644 --- a/benchmarks/heck-relay/convergence/heck-relay_optimized.fld +++ b/benchmarks/heck-relay/convergence/heck-relay_optimized.fld @@ -1028,25 +1028,25 @@ C Radius Eps Offset Charge Atm1 Lp(not used in MM3) C (ang) (kcal/mole) (ang) -6 - C1 1.9400 0.0560 0.0000 0000 O 2 - C2 1.9400 0.0560 0.0000 O200 O 1 + C1 2.1127 0.1671 0.0000 0000 O 2 + C2 2.0883 0.0544 0.0000 O200 O 1 C2 1.9600 0.0560 0.0000 0000 O 1 MM3 (JCC,1164,87) - C3 2.0400 0.0270 0.0000 0000 O 1 + C3 2.1954 0.1122 0.0000 0000 O 1 CP 1.9400 0.0560 0.0000 1.0000 0000 O 2 CR 1.9600 0.0560 0.0000 0000 O 2 O2 1.8200 0.0590 0.0000 0000 O 1 - O3 1.8200 0.0590 0.0000 0000 O 1 + O3 1.7477 0.0543 0.0000 0000 O 1 OM 1.8200 0.0590 0.0000 -1.0000 0000 O 2 OP 1.8200 0.0590 0.0000 1.0000 0000 A 3 Sp2 Oxonium, WCS (CU) OQ 1.8200 0.0590 0.0000 1.0000 0000 A 3 Sp3 Oxonium, WCS (CU) - H1 1.6200 0.0200 0.0000 SX00 O 3 + H1 1.7611 0.0011 0.0000 SX00 O 3 H1 1.6200 0.0200 -0.0770 0000 O 1 MM3 (JCC,1164,87) H2 1.6000 0.0160 0.0000 0000 O 1 H3 1.6000 0.0150 0.0000 N200 O 2 H3 1.6000 0.0180 0.0000 0000 O 1 H4 1.6000 0.0340 0.0000 0000 O 2 N1 1.9300 0.0430 0.0000 0000 O 2 - N2 1.9300 0.0430 0.0000 0000 O 2 + N2 2.0793 0.0936 0.0000 0000 O 2 N3 1.9300 0.0430 0.0000 0000 O 1 N4 1.9300 0.0430 0.0000 1.0000 0000 O 2 N5 1.9300 0.0430 0.0000 1.0000 0000 O 2 @@ -1054,13 +1054,13 @@ B3 2.1500 0.0140 0.0000 -1.0000 0000 O 2 SX 2.1500 0.2020 0.0000 0000 O 2 PX 2.2200 0.1680 0.0000 0000 O 2 - F0 1.7100 0.0750 0.0000 0000 O 2 + F0 1.8880 0.1792 0.0000 0000 O 2 Cl 2.0700 0.2400 0.0000 0000 O 2 Br 2.2200 0.3200 0.0000 0000 O 2 I0 2.3600 0.4240 0.0000 0000 O 2 Si 2.2900 0.1400 0.0000 0000 O 2 Z0 2.0000 0.6300 0.0000 2.0000 0000 A 2 WCS (CU) Barium - PD 1.7000 0.4140 0.0000 1.0000 0000 O 2 + PD 1.6338 0.3917 0.0000 1.0000 0000 O 2 END OF NONBONDED INTERACTIONS C C @@ -1864,26 +1864,26 @@ -2 aA 1 2 3 180.0000 45.0000 1 AA 3 1.3927 4.4976 0.7339 - 1 H1 3 1.0959 4.4976 0.7698 - 1 C3 4 1.5023 4.3748 1.3883 - 1 H1 4 1.0890 5.4145 0.4272 - 1 C3 5 1.5070 4.2280 -0.0536 - 1 H1 5 1.0937 5.2434 0.6075 - 1 2 3 2.0759 4.0671 -3.5269 - 1 2 5 2.0877 2.4577 -1.6173 + 1 H1 3 1.0637 4.4977 0.7698 + 1 C3 4 1.4532 4.3772 1.3883 + 1 H1 4 1.0651 5.4198 0.4272 + 1 C3 5 1.5864 4.2256 -0.0536 + 1 H1 5 1.2147 5.2437 0.6075 + 1 2 3 2.0030 4.1462 -3.5269 + 1 2 5 2.0095 2.3841 -1.6173 1 3 4 2.1101 2.3558 -1.5079 - 1 4 5 1.4146 6.2700 0.0000 - 2 1 2 3 93.7490 1.4790 + 1 4 5 1.4179 6.3611 0.0000 + 2 1 2 3 90.2967 1.9406 a2 1 2 3 169.5275 0.0000 2 1 2 5 173.7132 0.0000 a2 1 2 5 98.4584 0.8361 2 1 2 6 76.3339 0.9927 - 2 3 2 5 91.3826 0.4796 + 2 3 2 5 88.0613 -0.0880 2 2 3 AA 116.6215 0.7557 - 2 2 3 H1 109.7750 0.7557 + 2 2 3 H1 113.5758 0.9988 2 4 3 AA 111.7267 0.5083 2 4 3 H1 107.2035 0.5083 - 2 2 3 4 69.4819 0.3443 + 2 2 3 4 67.3452 -0.2159 2 H1 4 H1 114.6116 0.6350 2 H1 4 C0 114.9351 0.8771 2 C0 4 C0 111.4190 1.2871 @@ -1909,61 +1909,61 @@ a4 00 1 2 5 0.0000 0.0000 0.0000 4 00 1 2 6 0.0000 0.0000 0.0000 4 1 2 3 00 0.0000 0.0000 0.0000 a4 1 2 3 00 0.0000 0.0000 0.0000 - 4 1 2 3 4 0.0000 0.0000 0.0000 -a4 1 2 3 4 0.0000 0.0000 0.0000 + 4 1 2 3 4 -2.1659 2.1667 2.1638 +a4 1 2 3 4 -2.1659 2.1667 2.1638 4 5 2 3 00 0.0000 0.0000 0.0000 - 4 5 2 3 4 0.0000 0.0000 0.0000 - 4 1 2 5 4 0.0000 0.0000 0.0000 -a4 1 2 5 4 0.0000 0.0000 0.0000 - 4 1 2 5 H1 0.0000 0.0000 0.0000 -a4 1 2 5 H1 0.0000 0.0000 0.0000 - 4 1 2 5 C0 0.0000 0.0000 0.0000 -a4 1 2 5 C0 0.0000 0.0000 0.0000 - 4 3 2 5 4 0.0000 0.0000 0.0000 - 4 3 2 5 H1 0.0000 0.0000 0.0000 - 4 3 2 5 C0 0.0000 0.0000 0.0000 + 4 5 2 3 4 2.1668 2.1684 -2.1653 + 4 1 2 5 4 -2.1659 2.1667 2.1638 +a4 1 2 5 4 -2.1659 2.1667 2.1638 + 4 1 2 5 H1 -2.1636 2.1642 2.1602 +a4 1 2 5 H1 -2.1636 2.1642 2.1602 + 4 1 2 5 C0 -2.1657 -2.1626 2.1645 +a4 1 2 5 C0 -2.1657 -2.1626 2.1645 + 4 3 2 5 4 2.1668 2.1684 -2.1653 + 4 3 2 5 H1 2.1633 2.1638 -2.1592 + 4 3 2 5 C0 2.1668 2.1684 -2.1653 4 00 3 4 5 0.0000 0.0000 0.0000 4 00 3 4 H1 0.0000 0.0000 0.0000 4 00 3 4 C0 0.0000 0.0000 0.0000 - 4 2 3 4 5 0.0000 0.0000 0.0000 - 4 2 3 4 H1 0.0000 0.0000 0.0000 - 4 2 3 4 C0 0.0000 0.0000 0.0000 - 4 C0 4 5 C0 0.0000 1.0009 0.0000 - 4 C0 4 5 H1 0.0000 1.0009 0.0000 - 4 H1 4 5 C0 0.0000 1.0001 0.0000 - 4 H1 4 5 H1 0.0000 1.0008 0.0000 - 4 3 4 5 2 0.0000 0.0000 0.0000 - 4 3 4 5 H1 0.0000 0.0000 0.0000 - 4 3 4 5 C0 0.0000 0.0000 0.0000 - 4 H1 4 5 2 0.0000 0.0000 0.0000 - 4 C0 4 5 2 0.0000 0.0000 0.0000 + 4 2 3 4 5 -2.1649 -2.1662 -2.1675 + 4 2 3 4 H1 2.1652 -2.1648 2.1639 + 4 2 3 4 C0 -2.1649 -2.1662 -2.1675 + 4 C0 4 5 C0 1.1862 -1.2178 2.1644 + 4 C0 4 5 H1 -1.5134 -1.2179 -2.1645 + 4 H1 4 5 C0 -1.5134 -1.2186 -2.1645 + 4 H1 4 5 H1 -2.1648 -1.2188 -2.1655 + 4 3 4 5 2 -2.1649 -2.1662 -2.1675 + 4 3 4 5 H1 -2.1695 -2.1593 -2.1647 + 4 3 4 5 C0 1.1862 -2.1645 2.1644 + 4 H1 4 5 2 2.1652 -2.1648 2.1639 + 4 C0 4 5 2 -2.1649 -2.1662 -2.1675 4 00 4 C2 00 0.0000 0.0000 0.0000 - 4 C0 4 C3 C0 0.0000 0.0000 0.0002 - 4 C0 4 C3 03 0.0000 0.0000 0.0000 - 4 C0 4 C3 H1 0.0000 0.0000 0.0000 - 4 H1 4 C3 C0 0.0004 0.0000 0.0005 - 4 H1 4 C3 O3 0.0000 0.0000 0.0000 - 4 H1 4 C3 H1 0.0000 0.0000 0.0009 - 4 3 4 C3 C0 0.0000 0.0000 0.0000 - 4 3 4 C3 O3 0.0000 0.0000 0.0000 - 4 3 4 C3 H1 0.0000 0.0000 0.0000 - 4 5 4 C3 C0 0.0009 0.0000 -0.0006 - 4 5 4 C3 O3 0.0000 0.0000 0.0000 - 4 5 4 C3 H1 0.0000 0.0000 0.0000 + 4 C0 4 C3 C0 1.1862 -2.1645 2.1646 + 4 C0 4 C3 03 1.1862 -2.1645 2.1644 + 4 C0 4 C3 H1 -1.5134 -2.1646 -2.1645 + 4 H1 4 C3 C0 -1.5130 -2.1646 -2.1641 + 4 H1 4 C3 O3 -2.1645 2.1645 2.1644 + 4 H1 4 C3 H1 2.1642 -2.1638 2.1643 + 4 3 4 C3 C0 1.1862 -2.1645 2.1644 + 4 3 4 C3 O3 2.1644 -2.1646 -2.1638 + 4 3 4 C3 H1 -2.1638 -2.1637 -2.1596 + 4 5 4 C3 C0 1.1871 -2.1645 2.1638 + 4 5 4 C3 O3 2.1644 -2.1646 -2.1638 + 4 5 4 C3 H1 -2.1638 -2.1637 -2.1596 4 00 5 C2 00 0.0000 0.0000 0.0000 - 4 C0 5 C3 C0 0.0000 0.0000 0.0000 + 4 C0 5 C3 C0 1.1862 -2.1645 2.1644 4 C0 5 C3 O3 0.0000 0.0000 0.0000 - 4 C0 5 C3 H1 0.0000 0.0000 0.0009 - 4 H1 5 C3 C0 0.0000 0.0000 0.0005 - 4 H1 5 C3 O3 0.0000 0.0000 0.0008 - 4 H1 5 C3 H1 0.0000 0.0000 0.0008 + 4 C0 5 C3 H1 -1.5134 -2.1646 -2.1637 + 4 H1 5 C3 C0 -1.5134 -2.1646 -2.1641 + 4 H1 5 C3 O3 -2.1645 2.1645 2.1651 + 4 H1 5 C3 H1 2.1642 -2.1638 2.1642 4 2 5 C3 00 0.0000 0.0000 0.0000 - 4 2 5 C3 C0 0.0000 0.0000 0.0000 - 4 2 5 C3 O3 0.0000 0.0000 0.0000 - 4 2 5 C3 H1 0.0000 0.0000 0.0000 - 4 4 5 C3 C0 0.0000 0.0000 0.0004 - 4 4 5 C3 O3 0.0000 0.0000 -0.0002 - 4 4 5 C3 H1 0.0000 0.0000 0.0000 + 4 2 5 C3 C0 -2.1649 -2.1662 -2.1675 + 4 2 5 C3 O3 2.1646 2.1646 2.1646 + 4 2 5 C3 H1 2.1650 -2.1660 -2.1621 + 4 4 5 C3 C0 1.1862 -2.1645 2.1648 + 4 4 5 C3 O3 2.1644 -2.1646 -2.1640 + 4 4 5 C3 H1 -2.1638 -2.1637 -2.1596 5 3 2 00 00 0.0000 0.0000 5 5 4 00 00 0.0000 0.0000 5 4 5 00 00 0.0000 0.0000 @@ -1971,7 +1971,7 @@ a4 1 2 5 C0 0.0000 0.0000 0.0000 C Palladium pyridine OPT 9 PD.N2*AA -2 - 1 1 2 2.2249 1.6738 -3.5972 + 1 1 2 2.1454 1.6314 -3.5972 1 2 3 1.3408 3.7931 -2.9786 1 H1 3 1.0896 5.4813 0.1467 2 1 2 3 120.7554 1.6895 @@ -1982,20 +1982,20 @@ a4 1 2 5 C0 0.0000 0.0000 0.0000 C Palladium oxazoline OPT 9 PD.N2=C2-O3-C3-C3-2 -2 - 1 1 2 2.1787 3.7847 -2.7750 - 1 2 3 1.2843 9.8049 -1.8078 - 1 2 6 1.4721 3.9367 -1.9370 - 1 3 4 1.3267 7.3324 0.1915 - 1 4 5 1.4545 3.8716 -2.1837 - 2 1 2 3 112.4657 1.6204 - 2 1 2 6 139.9081 1.2907 + 1 1 2 2.0635 3.7680 -2.7750 + 1 2 3 1.2513 9.8141 -1.8078 + 1 2 6 1.5512 3.9395 -1.9370 + 1 3 4 1.2866 7.3321 0.1915 + 1 4 5 1.5393 3.8522 -2.1837 + 2 1 2 3 116.1201 1.4534 + 2 1 2 6 142.0778 1.3313 2 3 2 6 107.2357 1.5212 - 2 2 3 4 118.2162 0.9672 + 2 2 3 4 121.5598 1.1185 2 2 3 C2 122.6663 0.0183 2 4 3 C2 119.1109 0.7761 2 3 4 5 105.7675 1.6705 - 4 1 2 3 4 0.0000 5.8784 0.0000 - 4 1 2 3 C2 0.0000 2.4912 0.0000 + 4 1 2 3 4 2.1646 7.7249 2.1645 + 4 1 2 3 C2 2.1634 4.5185 2.1665 4 1 2 6 00 0.0000 0.0000 0.0000 5 2 00 00 00 0.0000 0.0000 -3 @@ -2005,12 +2005,12 @@ a4 1 2 5 C0 0.0000 0.0000 0.0000 aA 1 2 3 180.0000 45.0000 4 1 3 5 6 0.0000 40.0000 0.0000 a4 1 3 5 6 0.0000 40.0000 0.0000 - 4 3 5 6 1 0.0000 0.0000 0.0000 -a4 3 5 6 1 0.0000 0.0000 0.0000 - 4 3 1 6 5 0.0000 0.0000 0.0000 -a4 3 1 6 5 0.0000 0.0000 0.0000 - 4 6 1 3 5 0.0000 0.0000 0.0000 -a4 6 1 3 5 0.0000 0.0000 0.0000 + 4 3 5 6 1 -2.1659 2.1667 2.1638 +a4 3 5 6 1 -2.1659 2.1667 2.1638 + 4 3 1 6 5 -2.1646 2.1646 2.1619 +a4 3 1 6 5 -2.1646 2.1646 2.1619 + 4 6 1 3 5 2.1634 2.1621 2.1665 +a4 6 1 3 5 2.1634 2.1621 2.1665 4 1 3 5 2 0.0000 40.0000 0.0000 a4 1 3 5 2 0.0000 40.0000 0.0000 4 1 6 5 2 0.0000 0.0000 0.0000 @@ -2021,8 +2021,8 @@ a4 3 5 6 2 0.0000 0.0000 0.0000 a4 3 1 6 2 0.0000 0.0000 0.0000 4 5 6 1 2 0.0000 0.0000 0.0000 a4 5 6 1 2 0.0000 0.0000 0.0000 - 4 5 3 1 2 0.0000 0.0000 0.0000 -a4 5 3 1 2 0.0000 0.0000 0.0000 + 4 5 3 1 2 2.1634 2.1621 2.1665 +a4 5 3 1 2 2.1634 2.1621 2.1665 4 6 1 3 2 0.0000 0.0000 0.0000 a4 6 1 3 2 0.0000 0.0000 0.0000 4 6 5 3 2 0.0000 0.0000 0.0000 diff --git a/benchmarks/heck-relay/convergence/paper_metrics.json b/benchmarks/heck-relay/convergence/paper_metrics.json index ceff2cd..5edbe00 100644 --- a/benchmarks/heck-relay/convergence/paper_metrics.json +++ b/benchmarks/heck-relay/convergence/paper_metrics.json @@ -1,16 +1,13 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-27T23:11:26.865699+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system heck-relay --n-evals 10 --ratio-tol none --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T05:22:13.045666+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system heck-relay --n-evals 10 --ratio-tol none --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "86d848397f69832fef39104c337704373d60c857", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "a3cc8d7d540b66a896fd1b439cebdf49ddc7bc5c", + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": null, "maxiter": 500, "n_evals": 10, @@ -30,45 +27,45 @@ "seminario": { "bond_length": { "n_refs": 1140, - "r2": 0.9790319412096813, - "rmsd": 0.04728093475868026, - "mae": 0.027298790108083247 + "r2": 0.981038111369397, + "rmsd": 0.044962219041832396, + "mae": 0.026791195009444716 }, "bond_angle": { "n_refs": 2157, - "r2": 0.7786596184395878, - "rmsd": 8.087335271830058, - "mae": 5.237661196985309 + "r2": 0.8093155299739117, + "rmsd": 7.506418655976105, + "mae": 4.923241345978376 }, "eig_diagonal": { "n_refs": 3121, - "r2": -12.618267839869592, - "rmsd": 0.47733708251347695, - "mae": 0.34159681776745104 + "r2": -12.61826783986958, + "rmsd": 0.47733708251347673, + "mae": 0.3415968177674508 }, - "_objective_score": 3300583.661724017, + "_objective_score": 3134582.5069351243, "_total_refs": 6418 }, "optimized": { "bond_length": { "n_refs": 1140, - 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"git_sha": "a3cc8d7d540b66a896fd1b439cebdf49ddc7bc5c", + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, "n_evals": 10, @@ -30,15 +27,15 @@ "seminario": { "bond_length": { "n_refs": 457, - "r2": 0.8918097560733633, - "rmsd": 0.12865481616059454, - "mae": 0.05447425008974926 + "r2": 0.8878399832429736, + "rmsd": 0.1309938876386436, + "mae": 0.056730827782810744 }, "bond_angle": { "n_refs": 926, - "r2": 0.4454842381645594, - "rmsd": 16.688834857689724, - "mae": 11.022942698827642 + "r2": 0.4720641833946059, + "rmsd": 16.28394522678011, + "mae": 10.920052482235633 }, "eig_diagonal": { "n_refs": 1244, @@ -46,29 +43,29 @@ "rmsd": 0.371059418502375, "mae": 0.27255770882038477 }, - "_objective_score": 6468197.7295803, + "_objective_score": 6464571.330730133, "_total_refs": 2627 }, "optimized": { "bond_length": { "n_refs": 457, - "r2": 0.889696596952639, - "rmsd": 0.12990517558689313, - "mae": 0.05507317667934524 + "r2": 0.8218605385983645, + "rmsd": 0.165086692298655, + "mae": 0.08918042369119644 }, "bond_angle": { "n_refs": 926, - "r2": 0.4532236703623872, - "rmsd": 16.57196174992739, - "mae": 10.895252379752609 + "r2": 0.539784279740658, + "rmsd": 15.203717600159505, + "mae": 10.540916607350587 }, "eig_diagonal": { "n_refs": 1244, - "r2": -7.862431939033797, - "rmsd": 0.371059418502375, - "mae": 0.27255770882038477 + "r2": -12.852633990598438, + "rmsd": 0.4639094111501908, + "mae": 0.3188457087271904 }, - "_objective_score": 6440960.414222153, + "_objective_score": 5094628.513920791, "_total_refs": 2627 } } diff --git a/benchmarks/rh-1,4-conjugate-addition/convergence/rh-conjugate_optimized.fld b/benchmarks/rh-1,4-conjugate-addition/convergence/rh-conjugate_optimized.fld index 52fdc3c..ce90990 100644 --- a/benchmarks/rh-1,4-conjugate-addition/convergence/rh-conjugate_optimized.fld +++ b/benchmarks/rh-1,4-conjugate-addition/convergence/rh-conjugate_optimized.fld @@ -1,29 +1,29 @@ C OPT OPT Generated 9 AUTO - 1 C2 C2 1.4029 4.2857 - 1 C2 Rh 2.1588 7.2735 + 1 C2 C2 1.2897 4.2352 + 1 C2 Rh 2.6804 7.2823 1 C2 Rh 2.1416 9.3784 1 C2 C2 2.0139 0.1000 - 1 C2 C2 1.4426 5.1182 + 1 C2 C2 1.5092 5.1257 1 P3 Rh 2.2900 0.6460 1 C2 P3 1.8266 2.7043 - 1 C2 C2 1.3671 6.5627 + 1 C2 C2 1.2008 6.5603 1 H1 P3 1.4172 3.4759 1 C2 P3 1.8828 2.8618 1 D1 Rh 1.6670 0.3307 1 C2 D1 0.7515 2.8150 - 1 C2 C3 1.5151 4.0871 - 1 C2 C2 1.4500 0.1087 - 1 C2 H1 1.0911 5.4398 - 1 C2 C3 1.5152 4.2333 - 1 C2 H1 1.0931 5.3948 + 1 C2 C3 1.4845 4.0872 + 1 C2 C2 1.5004 0.1292 + 1 C2 H1 0.8982 5.4409 + 1 C2 C3 1.5136 4.2333 + 1 C2 H1 1.1415 5.3901 1 C2 N3 1.4000 1.0929 - 1 C2 O3 1.3603 3.2143 + 1 C2 O3 1.4096 3.2142 1 C2 C2 1.4664 4.5194 - 1 C2 O2 1.2233 11.2571 - 1 C2 C2 1.5118 2.2924 - 1 C2 O2 1.2091 12.1258 - 1 C2 N2 1.4057 3.1457 + 1 C2 O2 1.1920 11.2574 + 1 C2 C2 1.5112 2.2924 + 1 C2 O2 1.1990 12.1258 + 1 C2 N2 1.4049 3.1457 1 C3 C3 1.5177 4.4900 1 C3 C3 1.5177 4.4900 1 C3 C3 1.5197 4.4900 @@ -212,26 +212,26 @@ 1 C2 C2 1.4281 4.1874 2 C2 Rh Rh 103.9451 0.1000 2 C2 Rh Rh 179.1576 0.3338 - 2 C2 Rh P3 91.4500 0.1155 + 2 C2 Rh P3 94.1134 0.1948 2 C2 Rh P3 168.5500 0.1441 2 C2 Rh Rh 177.9734 0.2493 2 C2 Rh Rh 92.4672 1.0146 2 C2 Rh P3 171.1000 0.3382 2 C2 Rh P3 98.2000 0.1204 2 P3 Rh Rh 88.4398 0.1704 - 2 C2 Rh C2 82.7105 1.7386 + 2 C2 Rh C2 81.1113 1.5298 2 00 C2 Rh 125.9136 0.1465 2 00 C2 C2 111.8106 1.0335 - 2 C2 C2 Rh 63.1974 1.9528 - 2 C2 C2 C2 138.0284 0.1655 - 2 C2 C2 H1 97.3654 0.5226 + 2 C2 C2 Rh 62.2033 2.1951 + 2 C2 C2 C2 139.2918 0.4616 + 2 C2 C2 H1 99.8579 0.8079 2 C0 C2 C2 106.1287 0.6965 2 C2 C2 Rh 95.7288 0.1079 - 2 H1 C2 Rh 118.7199 0.4064 + 2 H1 C2 Rh 120.5630 0.6952 2 C0 C2 Rh 104.8147 0.6917 - 2 C2 P3 Rh 141.4756 0.1024 - 2 H1 P3 Rh 119.0886 0.5605 - 2 C2 P3 H1 100.5432 0.3827 + 2 C2 P3 Rh 138.1218 -0.2016 + 2 H1 P3 Rh 120.9207 0.6990 + 2 C2 P3 H1 102.9331 0.5878 2 C2 P3 C2 104.9099 0.2374 2 C2 P3 C2 102.6888 0.2042 2 P3 Rh P3 100.3107 0.4461 @@ -244,15 +244,15 @@ 2 C0 C2 D1 106.0000 0.9638 2 D1 C2 H1 122.9167 0.1014 2 C2 C2 H1 127.1757 0.4539 - 2 C2 C2 C3 125.9238 0.7655 - 2 C3 C2 H1 124.2707 0.5517 + 2 C2 C2 C3 123.0371 0.8803 + 2 C3 C2 H1 121.4344 0.5609 2 C0 C2 C3 115.0440 1.1480 2 C2 C2 H1 135.4688 0.4264 2 C2 C2 C3 134.8579 0.6224 2 C2 C2 C2 142.6819 0.2641 2 C2 C2 H1 137.0606 0.3353 2 C2 C2 C3 125.3438 0.7784 - 2 C2 C2 O2 124.9109 1.3998 + 2 C2 C2 O2 122.0564 1.3949 2 C2 C2 C2 112.5747 1.2296 2 C2 C2 O2 128.9297 0.5292 2 C2 C2 N2 104.6404 0.1001 @@ -545,36 +545,36 @@ 4 Rh Rh C2 00 0.0000 0.0000 0.0000 4 Rh Rh C2 C2 0.0000 4.0581 0.0000 4 C2 Rh C2 00 0.0000 0.0000 0.0000 - 4 C2 Rh C2 C2 0.0000 0.0000 0.0000 + 4 C2 Rh C2 C2 -1.2051 -1.2122 -1.1963 4 Rh Rh C2 H1 0.0000 0.0000 0.0000 4 Rh Rh C2 C0 0.0000 0.0000 1.7364 - 4 P3 Rh C2 C2 0.0000 -8.8108 0.0000 - 4 P3 Rh C2 C0 0.0000 -2.5212 0.0000 - 4 P3 Rh C2 H1 0.0000 0.0000 0.0000 - 4 C2 Rh C2 H1 0.0000 0.0000 0.0000 - 4 C2 Rh C2 C0 0.0000 0.0000 0.0000 - 4 C2 Rh P3 C2 0.0000 -0.3251 0.0000 + 4 P3 Rh C2 C2 1.2027 -7.3419 -1.1993 + 4 P3 Rh C2 C0 1.2027 -1.2415 -1.1993 + 4 P3 Rh C2 H1 -1.2026 -1.2056 1.2011 + 4 C2 Rh C2 H1 1.2040 -1.2081 -1.2139 + 4 C2 Rh C2 C0 -1.2051 -1.2122 -1.1963 + 4 C2 Rh P3 C2 -1.2035 -1.5113 1.2002 4 00 C2 C2 C2 0.0000 0.0000 0.0000 4 00 C2 C2 H1 0.0000 0.0000 0.0000 4 00 C2 C2 C3 0.0000 0.0000 0.0000 - 4 Rh C2 C2 C2 0.0000 0.0000 0.0000 - 4 Rh C2 C2 H1 0.0000 0.0000 0.0000 - 4 Rh C2 C2 C3 0.0000 0.0000 0.0000 + 4 Rh C2 C2 C2 1.2072 1.1987 -1.2083 + 4 Rh C2 C2 H1 -1.2069 1.1971 -1.2037 + 4 Rh C2 C2 C3 1.2072 1.1987 -1.2083 4 C2 C2 C2 H1 0.0000 0.0000 0.0000 - 4 C2 C2 C2 C0 0.0000 0.0000 0.0000 + 4 C2 C2 C2 C0 -1.2031 1.2031 -1.2032 4 C2 C2 C2 C2 0.0000 1.5500 0.0000 - 4 C2 C2 C2 Rh 0.0000 3.2626 0.0000 - 4 H1 C2 C2 Rh 0.0000 0.0000 0.0000 - 4 C0 C2 C2 Rh 0.0000 0.0000 0.0000 - 4 C2 C2 C3 C0 0.0000 0.0000 0.0000 + 4 C2 C2 C2 Rh 1.2072 4.3632 -1.2083 + 4 H1 C2 C2 Rh -1.2069 1.1971 -1.2037 + 4 C0 C2 C2 Rh 1.2072 1.1987 -1.2083 + 4 C2 C2 C3 C0 -1.2031 1.2031 -1.2032 4 C2 C2 C3 O3 0.0000 0.0000 0.0000 - 4 C2 C2 C3 H1 0.0000 0.0000 0.0000 + 4 C2 C2 C3 H1 -1.2038 1.2018 -1.2062 4 P3 Rh Rh C2 0.0000 0.0000 0.0000 4 P3 Rh Rh H1 0.0000 0.0000 0.0000 4 C2 Rh 00 00 0.0000 0.0000 0.0000 4 C2 C2 00 00 0.0000 0.0000 0.0000 - 4 Rh P3 C2 C2 0.0000 0.0000 0.0000 - 4 Rh P3 C2 H1 0.0000 1.7798 0.0000 + 4 Rh P3 C2 C2 1.2035 -1.2028 1.2023 + 4 Rh P3 C2 H1 -1.2031 0.5231 -1.2031 4 D1 Rh D1 C2 0.0000 0.0000 0.0000 4 Rh D1 C2 C2 0.0000 0.0000 0.0000 4 Rh D1 C2 C0 0.0000 0.0000 0.0000 @@ -585,29 +585,29 @@ 4 D1 C2 C2 C3 0.0000 0.0000 0.0000 4 D1 C2 C2 C2 0.0000 0.0000 0.0000 4 D1 C2 C2 H1 0.0000 0.0000 0.0000 - 4 C2 C2 C0 C0 0.0000 0.0000 0.0000 + 4 C2 C2 C0 C0 -1.2031 1.2031 -1.2032 4 D1 C2 C3 00 0.0000 0.0000 0.0000 - 4 C0 C2 C2 C0 0.0000 0.0000 0.0000 - 4 C0 C2 C2 C2 0.0000 0.0000 0.0000 - 4 C0 C2 C2 H1 0.0000 0.0000 0.0000 - 4 H1 C2 C2 C0 0.0000 0.0000 0.0000 + 4 C0 C2 C2 C0 -1.2031 1.2031 -1.2032 + 4 C0 C2 C2 C2 -1.2031 1.2031 -1.2032 + 4 C0 C2 C2 H1 0.0704 0.2843 0.6504 + 4 H1 C2 C2 C0 0.0704 0.2843 0.6504 4 H1 C2 C2 C2 0.0000 1.5500 0.0000 4 H1 C2 C2 H1 0.0000 1.5500 0.0000 - 4 C0 C2 C3 C0 0.0000 0.0000 0.0000 + 4 C0 C2 C3 C0 -1.2031 1.2031 -1.2032 4 C0 C2 C3 O3 0.0000 0.0000 0.0000 - 4 C0 C2 C3 H1 0.0000 0.0000 0.0000 - 4 H1 C2 C3 C0 0.0000 0.0000 0.0000 + 4 C0 C2 C3 H1 0.0704 0.2843 0.6504 + 4 H1 C2 C3 C0 0.0704 0.2843 0.6504 4 H1 C2 C3 O3 0.0000 0.0000 0.0000 - 4 H1 C2 C3 H1 0.0000 0.0000 0.0000 + 4 H1 C2 C3 H1 1.2040 1.2033 -1.2022 4 C0 C2 C2 O3 0.0000 0.0000 0.0000 4 C0 C2 C2 O2 0.0000 2.1371 0.0000 4 H1 C2 C2 O3 0.0000 1.4000 0.0000 4 H1 C2 C2 O2 0.0000 1.7000 0.0000 - 4 Rh C2 C2 C0 0.0000 0.0000 0.0000 + 4 Rh C2 C2 C0 1.2072 1.1987 -1.2083 4 Rh C2 C2 O2 0.0000 -2.6485 0.0000 4 Rh C2 C2 O3 0.0000 2.1410 0.0000 4 Rh C2 C2 N2 0.0000 0.0000 0.0000 - 4 Rh C2 C0 H1 0.0000 0.0000 0.0000 + 4 Rh C2 C0 H1 -1.2069 1.1971 -1.2037 4 C2 C2 C2 C3 0.0000 1.7000 0.0000 4 C2 C2 C2 O3 0.0000 16.2500 0.3000 4 C2 C2 C2 O2 0.0000 1.6500 0.0000 diff --git a/benchmarks/rh-1,4-conjugate-addition/convergence/validation_results.json b/benchmarks/rh-1,4-conjugate-addition/convergence/validation_results.json index 5d88179..41c5fe7 100644 --- a/benchmarks/rh-1,4-conjugate-addition/convergence/validation_results.json +++ b/benchmarks/rh-1,4-conjugate-addition/convergence/validation_results.json @@ -1,16 +1,13 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-27T22:37:23.173058+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system rh-conjugate --n-evals 10 --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T03:35:06.377361+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system rh-conjugate --n-evals 10 --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "86d848397f69832fef39104c337704373d60c857", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "a3cc8d7d540b66a896fd1b439cebdf49ddc7bc5c", + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, "n_evals": 10, @@ -30,23 +27,23 @@ "system": "rh-conjugate", "n_molecules": 10, "n_active_params": 488, - "initial_obj_score": 6468197.7295803, - "initial_jaxloss": 6532877.0146037415, - "ratio": 1.0099995837677707, + "initial_obj_score": 6464571.330730133, + "initial_jaxloss": 6441876.131475579, + "ratio": 0.9964892955629294, "ratio_status": "ok", "ratio_passes": true, "seminario": { "bond_length": { "n_refs": 457, - "r2": 0.8918097560733633, - "rmsd": 0.12865481616059454, - "mae": 0.05447425008974926 + "r2": 0.8878399832429736, + "rmsd": 0.1309938876386436, + "mae": 0.056730827782810744 }, "bond_angle": { "n_refs": 926, - "r2": 0.4454842381645594, - "rmsd": 16.688834857689724, - "mae": 11.022942698827642 + "r2": 0.4720641833946059, + "rmsd": 16.28394522678011, + "mae": 10.920052482235633 }, "eig_diagonal": { "n_refs": 1244, @@ -55,41 +52,41 @@ "mae": 0.27255770882038477 } }, - "final_obj_score": 6440960.414222153, - "initial_obj_score_mean": 6430213.26266556, - "initial_obj_score_ci95": 26092.524294256793, - "final_obj_score_mean": 6435380.490532473, - "final_obj_score_ci95": 49696.31504475936, - "improvement_pct_mean": -0.08035857685957382, - "improvement_significant": false, - "final_optimizer_score": 6065297.681528205, - "initial_optimizer_score": 6349713.260742212, - "n_iterations": 1, + "final_obj_score": 5094628.513920791, + "initial_obj_score_mean": 6293272.170675544, + "initial_obj_score_ci95": 163838.62240465957, + "final_obj_score_mean": 5160404.119757806, + "final_obj_score_ci95": 98890.10869785814, + "improvement_pct_mean": 18.00125626532583, + "improvement_significant": true, + "final_optimizer_score": 5029235.926389622, + "initial_optimizer_score": 6145399.644865497, + "n_iterations": 4, "n_evaluations": 2, "converged": true, "message": "CONVERGENCE: RELATIVE REDUCTION OF F <= FACTR*EPSMCH", "jac_mode": "jax_loss", - "opt_time_s": 627.7275389070273, - "improvement_pct": 0.4210958986857416, - "surrogate_improvement_pct": 4.4791877606889186, + "opt_time_s": 690.7553385489737, + "improvement_pct": 21.191549241589314, + "surrogate_improvement_pct": 18.162589627648284, "optimized": { "bond_length": { "n_refs": 457, - "r2": 0.889696596952639, - "rmsd": 0.12990517558689313, - "mae": 0.05507317667934524 + "r2": 0.8218605385983645, + "rmsd": 0.165086692298655, + "mae": 0.08918042369119644 }, "bond_angle": { "n_refs": 926, - "r2": 0.4532236703623872, - "rmsd": 16.57196174992739, - "mae": 10.895252379752609 + "r2": 0.539784279740658, + "rmsd": 15.203717600159505, + "mae": 10.540916607350587 }, "eig_diagonal": { "n_refs": 1244, - "r2": -7.862431939033797, - "rmsd": 0.371059418502375, - "mae": 0.27255770882038477 + "r2": -12.852633990598438, + "rmsd": 0.4639094111501908, + "mae": 0.3188457087271904 } } } diff --git a/benchmarks/rh-enamide/convergence/paper_metrics.json b/benchmarks/rh-enamide/convergence/paper_metrics.json index 8c1579b..fcaad82 100644 --- a/benchmarks/rh-enamide/convergence/paper_metrics.json +++ b/benchmarks/rh-enamide/convergence/paper_metrics.json @@ -1,18 +1,16 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-26T22:46:25.236777+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system rh-enamide --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T06:49:46.280315+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system rh-enamide --n-evals 5 --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "85dc8c98957b7aee8ee29116da24a36c88817447", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "8b0fcb7942146e7fdecd756852657f7dad98013b", + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, + "n_evals": 5, "skip_optimization": false, "devices": { "jax_devices": [ @@ -29,15 +27,15 @@ "seminario": { "bond_length": { "n_refs": 500, - "r2": 0.9864962858450346, - "rmsd": 0.04320788860589175, - "mae": 0.0251747484635123 + "r2": 0.9865314845773111, + "rmsd": 0.04315153909906321, + "mae": 0.02517861864758527 }, "bond_angle": { "n_refs": 1050, - "r2": 0.9177254761065198, - "rmsd": 4.308550384235292, - "mae": 3.0856015104156227 + "r2": 0.9177322630486145, + "rmsd": 4.3083726713561274, + "mae": 3.082784453144462 }, "eig_diagonal": { "n_refs": 1395, @@ -45,29 +43,29 @@ "rmsd": 0.07334972382795417, "mae": 0.03795068177034179 }, - "_objective_score": 486295.0664245664, + "_objective_score": 489228.91097170254, "_total_refs": 2945 }, "optimized": { "bond_length": { "n_refs": 500, - "r2": 0.9891595415020878, - "rmsd": 0.03871330525882892, - "mae": 0.025929691235645157 + "r2": 0.9892292358484726, + "rmsd": 0.03858865882035943, + "mae": 0.026085829029484264 }, "bond_angle": { "n_refs": 1050, - "r2": 0.9542284994626772, - "rmsd": 3.2136313999367676, - "mae": 2.578901077082402 + "r2": 0.9544536171710511, + "rmsd": 3.205718866468329, + "mae": 2.576282648118119 }, "eig_diagonal": { "n_refs": 1395, - "r2": 0.9684793549267889, - "rmsd": 0.06740309270086962, - "mae": 0.03455681170685376 + "r2": 0.9682801723470084, + "rmsd": 0.06761572126942914, + "mae": 0.034760003039555884 }, - "_objective_score": 270624.4478166911, + "_objective_score": 269852.04848086444, "_total_refs": 2945 } } diff --git a/benchmarks/rh-enamide/convergence/rh-enamide_optimized.fld b/benchmarks/rh-enamide/convergence/rh-enamide_optimized.fld index 80e21b5..7eef585 100644 --- a/benchmarks/rh-enamide/convergence/rh-enamide_optimized.fld +++ b/benchmarks/rh-enamide/convergence/rh-enamide_optimized.fld @@ -1029,39 +1029,39 @@ C Radius Eps Offset Charge Atm1 Lp(not used in MM3) C (ang) (kcal/mole) (ang) -6 - C1 2.0468 0.2735 0.0000 0000 O 2 - C2 1.8994 0.0183 0.0000 O200 O 1 + C1 2.0601 0.2693 0.0000 0000 O 2 + C2 1.8981 0.0220 0.0000 O200 O 1 C2 1.9600 0.0560 0.0000 0000 O 1 MM3 (JCC,1164,87) - C3 1.9898 0.0432 0.0000 0000 O 1 + C3 2.0108 0.0366 0.0000 0000 O 1 CP 1.9400 0.0560 0.0000 1.0000 0000 O 2 CR 1.9600 0.0560 0.0000 0000 O 2 - O2 1.7937 0.0258 0.0000 0000 O 1 + O2 1.7933 0.0258 0.0000 0000 O 1 O3 1.8200 0.0590 0.0000 0000 O 1 OM 1.8200 0.0590 0.0000 -1.0000 0000 O 2 OP 1.8200 0.0590 0.0000 1.0000 0000 A 3 Sp2 Oxonium, WCS (CU) OQ 1.8200 0.0590 0.0000 1.0000 0000 A 3 Sp3 Oxonium, WCS (CU) - H1 1.5804 0.0338 0.0000 SX00 O 3 + H1 1.5184 0.0534 0.0000 SX00 O 3 H1 1.6200 0.0200 -0.0770 0000 O 1 MM3 (JCC,1164,87) H2 1.6000 0.0160 0.0000 0000 O 1 - H3 1.5952 0.0431 0.0000 N200 O 2 + H3 1.6016 0.0425 0.0000 N200 O 2 H3 1.6000 0.0180 0.0000 0000 O 1 H4 1.6000 0.0340 0.0000 0000 O 2 - N1 1.9636 0.0925 0.0000 0000 O 2 - N2 1.9231 0.0010 0.0000 0000 O 2 + N1 1.9626 0.0774 0.0000 0000 O 2 + N2 1.9201 0.0010 0.0000 0000 O 2 N3 1.9300 0.0430 0.0000 0000 O 1 N4 1.9300 0.0430 0.0000 1.0000 0000 O 2 N5 1.9300 0.0430 0.0000 1.0000 0000 O 2 B2 2.1500 0.0140 0.0000 0000 O 2 B3 2.1500 0.0140 0.0000 -1.0000 0000 O 2 SX 2.1500 0.2020 0.0000 0000 O 2 - PX 2.3662 0.3411 0.0000 0000 O 2 + PX 2.3664 0.3352 0.0000 0000 O 2 F0 1.7100 0.0750 0.0000 0000 O 2 Cl 2.0700 0.2400 0.0000 0000 O 2 Br 2.2200 0.3200 0.0000 0000 O 2 I0 2.3600 0.4240 0.0000 0000 O 2 Si 2.2900 0.1400 0.0000 0000 O 2 Z0 2.0000 0.6300 0.0000 2.0000 0000 A 2 WCS (CU) Barium - RH 2.8543 0.3114 0.0000 1.0000 0000 O 2 Donoghue + RH 2.8519 0.3003 0.0000 1.0000 0000 O 2 Donoghue H5 1.6200 0.0200 -0.0770 0000 O 1 Donoghue H6 1.6200 0.0200 -0.0770 0000 O 1 Donoghue H7 1.6200 0.0200 -0.0770 0000 O 1 Donoghue @@ -1857,36 +1857,36 @@ 9 HX-RH(-PX)-HX.C2*C2(.2)-N2-C2=O2.2 -2 aA 3 2 9 180.0000 45.0000 - 1 1 2 1.5954 2.5782 -0.4611 - 1 2 3 2.3623 5.0705 -6.6928 -a1 2 3 2.1239 1.5366 -5.0068 - 1 2 4 1.3830 1.6053 -1.5657 - 1 2 6 2.3184 0.0690 1.8318 - 1 2 9 2.1969 1.7061 0.6528 - 1 4 5 1.5957 21.9463 -1.3716 - 1 5 6 1.4482 4.1850 -1.5340 - 2 1 2 3 86.0426 0.7638 -a2 1 2 3 83.9645 0.4832 - 2 1 2 4 84.8621 0.0401 - 2 1 2 6 168.6283 0.3001 - 2 1 2 9 93.6543 1.2408 - 2 3 2 4 168.7550 0.0383 -a2 3 2 4 89.4722 0.0047 - 2 3 2 6 108.3012 0.2254 -a2 3 2 6 114.3247 1.2430 - 2 3 2 9 90.0410 0.6485 -a2 3 2 9 169.9912 0.1163 - 2 4 2 6 86.1561 0.8564 - 2 4 2 9 92.8006 0.9981 + 1 1 2 1.5943 2.5782 -0.4611 + 1 2 3 2.3591 5.0705 -6.6928 +a1 2 3 2.1317 1.5370 -5.0068 + 1 2 4 1.3874 1.6052 -1.5657 + 1 2 6 2.3183 0.0734 1.8318 + 1 2 9 2.1955 1.7056 0.6528 + 1 4 5 1.6008 21.9463 -1.3716 + 1 5 6 1.4570 4.1849 -1.5340 + 2 1 2 3 86.0814 0.7644 +a2 1 2 3 83.9421 0.4830 + 2 1 2 4 84.8621 0.0427 + 2 1 2 6 168.6326 0.3020 + 2 1 2 9 93.6899 1.2408 + 2 3 2 4 168.7550 0.0409 +a2 3 2 4 89.4722 0.0049 + 2 3 2 6 108.2690 0.2278 +a2 3 2 6 114.3522 1.2430 + 2 3 2 9 90.0164 0.6494 +a2 3 2 9 169.9816 0.1164 + 2 4 2 6 86.1948 0.8589 + 2 4 2 9 92.8365 0.9986 2 6 2 9 71.8497 0.0009 - 2 2 4 5 91.2733 2.3458 - 2 4 5 00 94.8234 0.1844 - 2 6 5 4 113.3287 0.0076 - 2 2 6 C0 164.1852 -0.0452 + 2 2 4 5 91.2482 2.3460 + 2 4 5 00 94.8582 0.1885 + 2 6 5 4 113.3287 0.0081 + 2 2 6 C0 164.1303 -0.0493 2 2 6 C2 111.9420 2.4856 - 2 2 6 5 71.6544 5.7727 - 2 2 6 7 106.2869 0.9991 - 2 2 9 8 115.0263 1.0585 + 2 2 6 5 71.6990 5.7730 + 2 2 6 7 106.3173 1.0028 + 2 2 9 8 114.9910 1.0584 4 00 2 3 00 0.0000 0.0000 0.0000 4 00 2 4 00 0.0000 0.0000 0.0000 4 00 2 6 00 0.0000 0.0000 0.0000 @@ -1894,7 +1894,7 @@ a2 3 2 9 169.9912 0.1163 4 2 4 5 00 0.0000 0.0000 0.0000 4 4 5 00 00 0.0000 0.0000 0.0000 4 C0 5 6 2 0.0000 0.0000 0.0000 - 4 H1 5 6 2 -0.2388 -0.2377 -0.2872 + 4 H1 5 6 2 -0.2561 -0.2546 -0.2989 4 4 5 6 2 0.0000 0.0000 0.0000 4 2 6 C2 O2 0.0000 0.0000 0.0000 4 2 6 C2 O3 0.0000 0.0000 0.0000 @@ -1906,8 +1906,8 @@ a2 3 2 9 169.9912 0.1163 C Rhodium catalyzed hydrogenation of enamides (RhH3-E / Eric) OPT 9 RH-PX -2 - 2 2 1 PX 85.6537 4.7578 - 4 1 2 C2 C0 -0.2847 0.2994 -0.2457 + 2 2 1 PX 85.6305 4.7577 + 4 1 2 C2 C0 -0.2997 0.3197 -0.2601 -3 diff --git a/benchmarks/rh-enamide/convergence/validation_results.json b/benchmarks/rh-enamide/convergence/validation_results.json index f4d7b84..0e655f1 100644 --- a/benchmarks/rh-enamide/convergence/validation_results.json +++ b/benchmarks/rh-enamide/convergence/validation_results.json @@ -1,18 +1,16 @@ { "provenance": { "generator": "scripts/regenerate_convergence_results.py", - "timestamp_utc": "2026-05-26T22:46:25.236777+00:00", - "command_line": "scripts/regenerate_convergence_results.py --system rh-enamide --output-dir /home/eric/repos/q2mm-data/benchmarks --log-level INFO", + "timestamp_utc": "2026-05-28T06:49:46.280315+00:00", + "command_line": "scripts/regenerate_convergence_results.py --system rh-enamide --n-evals 5 --output-dir /tmp/q2mm-fix-test", "q2mm": { - "git_sha": "85dc8c98957b7aee8ee29116da24a36c88817447", - "git_dirty": false - }, - "q2mm_data": { - "git_sha": "8b0fcb7942146e7fdecd756852657f7dad98013b", + "git_sha": "855c0868992e000e7afeb12aa5f1e1f4fd58c94c", "git_dirty": true }, + "q2mm_data": {}, "ratio_tol": 0.15, "maxiter": 500, + "n_evals": 5, "skip_optimization": false, "devices": { "jax_devices": [ @@ -29,23 +27,23 @@ "system": "rh-enamide", "n_molecules": 9, "n_active_params": 182, - "initial_obj_score": 486295.0664245664, - "initial_jaxloss": 519376.83690932376, - "ratio": 1.0680281844683057, + "initial_obj_score": 489228.91097170254, + "initial_jaxloss": 520131.89571518067, + "ratio": 1.0631667181771798, "ratio_status": "ok", "ratio_passes": true, "seminario": { "bond_length": { "n_refs": 500, - "r2": 0.9864962858450346, - "rmsd": 0.04320788860589175, - "mae": 0.0251747484635123 + "r2": 0.9865314845773111, + "rmsd": 0.04315153909906321, + "mae": 0.02517861864758527 }, "bond_angle": { "n_refs": 1050, - "r2": 0.9177254761065198, - "rmsd": 4.308550384235292, - "mae": 3.0856015104156227 + "r2": 0.9177322630486145, + "rmsd": 4.3083726713561274, + "mae": 3.082784453144462 }, "eig_diagonal": { "n_refs": 1395, @@ -54,32 +52,41 @@ "mae": 0.03795068177034179 } }, - "final_obj_score": 270624.4478166911, - "improvement_pct": 44.6649498405418, - "n_iterations": 15, + "final_obj_score": 269852.04848086444, + "initial_obj_score_mean": 488547.71596995916, + "initial_obj_score_ci95": 1078.151492464324, + "final_obj_score_mean": 270003.16644391743, + "final_obj_score_ci95": 341.4977409309725, + "improvement_pct_mean": 44.73351166776922, + "improvement_significant": true, + "final_optimizer_score": 269410.10642179585, + "initial_optimizer_score": 486178.6225804873, + "n_iterations": 13, "n_evaluations": 2, "converged": true, "message": "CONVERGENCE: RELATIVE REDUCTION OF F <= FACTR*EPSMCH", "jac_mode": "jax_loss", - "opt_time_s": 739.1627012130048, + "opt_time_s": 710.113396589004, + "improvement_pct": 44.841352906784174, + "surrogate_improvement_pct": 44.58618830423898, "optimized": { "bond_length": { "n_refs": 500, - "r2": 0.9891595415020878, - "rmsd": 0.03871330525882892, - "mae": 0.025929691235645157 + "r2": 0.9892292358484726, + "rmsd": 0.03858865882035943, + "mae": 0.026085829029484264 }, "bond_angle": { "n_refs": 1050, - "r2": 0.9542284994626772, - "rmsd": 3.2136313999367676, - "mae": 2.578901077082402 + "r2": 0.9544536171710511, + "rmsd": 3.205718866468329, + "mae": 2.576282648118119 }, "eig_diagonal": { "n_refs": 1395, - "r2": 0.9684793549267889, - "rmsd": 0.06740309270086962, - "mae": 0.03455681170685376 + "r2": 0.9682801723470084, + "rmsd": 0.06761572126942914, + "mae": 0.034760003039555884 } } }