Upload DFT-relaxed glycine PT dataset

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/README.md

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+# ORCA wB97X-D3/6-31G(d) Glycine Proton-Transfer DFT-Relaxed Scan
+
+This folder contains 579 ORCA analytical Hessian calculations and matching EnGrad calculations for a 2D glycine intramolecular proton-transfer scan.
+
+- Source reaction: Transition1x `test` split, `sample_id=5`, `rxn1961`
+- Formula: `C2H5NO2`
+- Method: wB97X-D3
+- Basis: 6-31G(d)
+- ORCA version: 6.1.1
+- Geometry source: constrained DFT optimizations initialized from the GFN2-xTB constrained-relaxed scan.
+- DFT optimization route: `! wB97X-D3 6-31G(d) TightSCF Opt`
+- ORCA Freq route: `! wB97X-D3 6-31G(d) TightSCF Freq`
+- ORCA EnGrad route: `! wB97X-D3 6-31G(d) TightSCF EnGrad`
+- Grid coordinates: `s = q_nh - q_oh`, `sigma = q_nh + q_oh` (Angstrom)
+- Bond constraints during DFT optimization: fixed `q_nh = d(N4,H9)`, `q_oh = d(O3,H9)` at each grid node.
+- Geometry files: `xyz/*.xyz` in Angstrom
+- Targets: `h5/glycine_pt_dft_relaxed.h5`
+- Diagnostics: `diagnostics/orca_energies.csv` and `.parquet`
+- Raw ORCA files: `raw/orca_outputs.tar.gz` containing Freq and EnGrad `.out`, `.hess`, `.engrad`, and `.inp` files.
+
+The HDF5 file uses atomic units for model targets: `coordinates_bohr`, `energy_hartree`, `gradient_hartree_per_bohr`, `forces_hartree_per_bohr`, and `hessian_hartree_per_bohr2`.
+
+Scan descriptors are stored as `s`, `sigma`, `q_nh_angstrom`, `q_oh_angstrom`, plus target grid indices `i_s`, `i_sigma`. The original xTB-relaxed bond lengths are retained as `q_nh_xtb_angstrom` and `q_oh_xtb_angstrom`.

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/diagnostics/metadata.json

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+{
+  "description": "GFN2-xTB constrained-relaxed 2D glycine proton-transfer scan in (s, sigma)",
+  "xtb_method": "GFN2-xTB",
+  "n_atom": 4,
+  "o_atom": 3,
+  "h_atom": 9,
+  "charge": 0,
+  "multiplicity": 1,
+  "orca_freq_route": "! wB97X-D3 6-31G(d) TightSCF Grid5 FinalGrid6 Freq",
+  "orca_engrad_route": "! wB97X-D3 6-31G(d) TightSCF EnGrad",
+  "fmax": 0.1,
+  "max_steps": 300,
+  "s_range": [
+    -2.16,
+    1.8
+  ],
+  "n_s": 34,
+  "sigma_range": [
+    2.4,
+    4.1
+  ],
+  "n_sigma": 25,
+  "q_bounds": [
+    0.85,
+    2.75
+  ],
+  "energy_ceiling_kcal": null,
+  "n_nodes_written": 579,
+  "n_skipped_q_bounds": 271,
+  "n_skipped_placement": 0,
+  "references": [
+    {
+      "label": "reactant",
+      "q_nh": 1.005210762796859,
+      "q_oh": 2.5250472712227414,
+      "s": -1.5198365084258825,
+      "sigma": 3.5302580340196004,
+      "energy_ev": -487.1356265076903,
+      "converged": true
+    },
+    {
+      "label": "ts",
+      "q_nh": 2.2682526586060874,
+      "q_oh": 0.9672372245950958,
+      "s": 1.3010154340109916,
+      "sigma": 3.235489883201183,
+      "energy_ev": -486.56487517562977,
+      "converged": true
+    },
+    {
+      "label": "product",
+      "q_nh": 2.2689818947481313,
+      "q_oh": 0.9658311220383046,
+      "s": 1.3031507727098268,
+      "sigma": 3.2348130167864357,
+      "energy_ev": -486.5660247818939,
+      "converged": true
+    }
+  ],
+  "ts_xyz": "/lustre/fs12/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/hip/runs/glycine_pt_scan_n36/xyz/reference_ts.xyz",
+  "reactant_xyz": "/lustre/fs12/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/hip/runs/glycine_pt_scan_n36/xyz/reference_reactant.xyz",
+  "product_xyz": "/lustre/fs12/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/hip/runs/glycine_pt_scan_n36/xyz/reference_product.xyz"
+}

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/diagnostics/orca_energies.parquet

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+size 72086

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/diagnostics/stationary_points.json

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+{
+  "reactant": {
+    "q_nh": 1.0052107627392792,
+    "q_oh": 2.525047271189948,
+    "s": -1.5198365084506689,
+    "sigma": 3.5302580339292273
+  },
+  "product": {
+    "q_nh": 2.268981894761696,
+    "q_oh": 0.9658311220504712,
+    "s": 1.3031507727112248,
+    "sigma": 3.234813016812167
+  },
+  "ts": {
+    "q_nh": 1.3348248354527743,
+    "q_oh": 1.324860251741224,
+    "s": 0.00996458371155029,
+    "sigma": 2.6596850871939983
+  }
+}

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/diagnostics/ts_xtb_saddle.json

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+{
+  "method": "GFN2-xTB Sella order-1 saddle",
+  "seed": "runs/glycine_pt_scan_n36/xyz/reference_ts.xyz",
+  "q_nh": 1.3348248354527743,
+  "q_oh": 1.324860251741224,
+  "s": 0.00996458371155029,
+  "sigma": 2.6596850871939983,
+  "n_imaginary": 1,
+  "lowest_freqs_cm1": [
+    -1791.0207386789293,
+    -3.5015290270315735e-05,
+    -1.8063895480947972e-05,
+    -1.146715003925726e-05,
+    1.508997219678165e-05,
+    1.9078492916146392e-05
+  ],
+  "softest_mode_pt_alignment": 0.9619865914879778,
+  "fmax_reached": 0.00847284144152444
+}

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/h5/glycine_pt_dft_relaxed.h5

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+version https://git-lfs.github.com/spec/v1
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+size 4398448

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/raw/orca_optimization_outputs.tar.gz

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+version https://git-lfs.github.com/spec/v1
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+size 29984884

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/raw/orca_outputs.tar.gz

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+version https://git-lfs.github.com/spec/v1
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+size 35177162

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/summary.json

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+{
+  "dataset": "orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579",
+  "num_samples": 579,
+  "atom_counts": {
+    "min": 10,
+    "max": 10
+  },
+  "source": {
+    "transition1x_split": "test",
+    "transition1x_sample_id": 5,
+    "rxn": "rxn1961",
+    "formula": "C2H5NO2"
+  },
+  "method": "wB97X-D3",
+  "basis": "6-31G(d)",
+  "orca_version": "6.1.1",
+  "orca_opt_route": "! wB97X-D3 6-31G(d) TightSCF Opt",
+  "orca_freq_route": "! wB97X-D3 6-31G(d) TightSCF Freq",
+  "orca_engrad_route": "! wB97X-D3 6-31G(d) TightSCF EnGrad",
+  "geometry_source": "DFT constrained optimization from GFN2-xTB constrained-relaxed scan geometries",
+  "scan_coordinates": {
+    "s": {
+      "description": "q_nh - q_oh reaction coordinate (A)"
+    },
+    "sigma": {
+      "description": "q_nh + q_oh donor-acceptor compression (A)"
+    },
+    "q_nh_angstrom": {
+      "atoms": [
+        4,
+        9
+      ],
+      "description": "DFT-optimized N4-H9 distance"
+    },
+    "q_oh_angstrom": {
+      "atoms": [
+        3,
+        9
+      ],
+      "description": "DFT-optimized O3-H9 distance"
+    }
+  },
+  "h5_datasets": [
+    "atomic_numbers",
+    "coordinates_bohr",
+    "energy_hartree",
+    "forces_hartree_per_bohr",
+    "gradient_hartree_per_bohr",
+    "grid_id",
+    "hessian_hartree_per_bohr2",
+    "i_s",
+    "i_sigma",
+    "q_nh_angstrom",
+    "q_nh_target_angstrom",
+    "q_nh_xtb_angstrom",
+    "q_oh_angstrom",
+    "q_oh_target_angstrom",
+    "q_oh_xtb_angstrom",
+    "s",
+    "sigma",
+    "symbols",
+    "xtb_converged",
+    "xtb_energy_ev"
+  ]
+}

orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0000_s_-1.800_sig_3.533_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0001_s_-1.800_sig_3.604_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0002_s_-1.800_sig_3.675_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0003_s_-1.680_sig_3.392_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0004_s_-1.680_sig_3.462_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0005_s_-1.680_sig_3.533_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0006_s_-1.680_sig_3.604_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0007_s_-1.680_sig_3.675_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0010_s_-1.560_sig_3.321_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0011_s_-1.560_sig_3.392_dft_opt.xyz

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+Coordinates from ORCA-job grid_0011_s_-1.560_sig_3.392_dft_opt E -284.348668375202
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0012_s_-1.560_sig_3.462_dft_opt.xyz

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+Coordinates from ORCA-job grid_0012_s_-1.560_sig_3.462_dft_opt E -284.354457136905
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0013_s_-1.560_sig_3.533_dft_opt.xyz

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+Coordinates from ORCA-job grid_0013_s_-1.560_sig_3.533_dft_opt E -284.357024470903
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0014_s_-1.560_sig_3.604_dft_opt.xyz

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+Coordinates from ORCA-job grid_0014_s_-1.560_sig_3.604_dft_opt E -284.357006815171
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0015_s_-1.560_sig_3.675_dft_opt.xyz

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+Coordinates from ORCA-job grid_0015_s_-1.560_sig_3.675_dft_opt E -284.354911508374
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0016_s_-1.560_sig_3.746_dft_opt.xyz

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+Coordinates from ORCA-job grid_0016_s_-1.560_sig_3.746_dft_opt E -284.351162198600
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0017_s_-1.560_sig_3.817_dft_opt.xyz

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+Coordinates from ORCA-job grid_0017_s_-1.560_sig_3.817_dft_opt E -284.346106059358
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0018_s_-1.560_sig_3.887_dft_opt.xyz

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+Coordinates from ORCA-job grid_0018_s_-1.560_sig_3.887_dft_opt E -284.340024663638
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0019_s_-1.440_sig_3.179_dft_opt.xyz

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+Coordinates from ORCA-job grid_0019_s_-1.440_sig_3.179_dft_opt E -284.332907471256
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0020_s_-1.440_sig_3.250_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0020_s_-1.440_sig_3.250_dft_opt E -284.344555875630
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0021_s_-1.440_sig_3.321_dft_opt.xyz

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+Coordinates from ORCA-job grid_0021_s_-1.440_sig_3.321_dft_opt E -284.351897239748
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0022_s_-1.440_sig_3.392_dft_opt.xyz

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+Coordinates from ORCA-job grid_0022_s_-1.440_sig_3.392_dft_opt E -284.355762643862
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0023_s_-1.440_sig_3.462_dft_opt.xyz

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+Coordinates from ORCA-job grid_0023_s_-1.440_sig_3.462_dft_opt E -284.356827832877
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0024_s_-1.440_sig_3.533_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0025_s_-1.440_sig_3.604_dft_opt.xyz

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+Coordinates from ORCA-job grid_0025_s_-1.440_sig_3.604_dft_opt E -284.352650215974
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0026_s_-1.440_sig_3.675_dft_opt.xyz

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+Coordinates from ORCA-job grid_0026_s_-1.440_sig_3.675_dft_opt E -284.348224325964
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0027_s_-1.440_sig_3.746_dft_opt.xyz

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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0028_s_-1.440_sig_3.817_dft_opt.xyz

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+Coordinates from ORCA-job grid_0028_s_-1.440_sig_3.817_dft_opt E -284.336232872996
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0029_s_-1.440_sig_3.887_dft_opt.xyz

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+Coordinates from ORCA-job grid_0029_s_-1.440_sig_3.887_dft_opt E -284.330409443160
+  C           1.51476445176689      0.09836778933719     -0.09247772749809
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0030_s_-1.440_sig_3.958_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0030_s_-1.440_sig_3.958_dft_opt E -284.323050496817
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0031_s_-1.440_sig_4.029_dft_opt.xyz

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+Coordinates from ORCA-job grid_0031_s_-1.440_sig_4.029_dft_opt E -284.315368240513
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0032_s_-1.320_sig_3.037_dft_opt.xyz

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+Coordinates from ORCA-job grid_0032_s_-1.320_sig_3.037_dft_opt E -284.324090414764
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0033_s_-1.320_sig_3.108_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0033_s_-1.320_sig_3.108_dft_opt E -284.337843993739
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0034_s_-1.320_sig_3.179_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0034_s_-1.320_sig_3.179_dft_opt E -284.346944843351
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0035_s_-1.320_sig_3.250_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0035_s_-1.320_sig_3.250_dft_opt E -284.352281865481
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orca_wb97x_d3_631gd_glycine_pt_dft_relaxed_579/xyz/grid_0036_s_-1.320_sig_3.321_dft_opt.xyz

@@ -0,0 +1,12 @@
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+Coordinates from ORCA-job grid_0036_s_-1.320_sig_3.321_dft_opt E -284.354579081525
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