Merge pull request #401 from openforcefield/not-another-compute-spec

adding third compute expansion
openforcefield · Nov 7, 2024 · 775900e · 775900e
2 parents 44efa60 + e391e56
commit 775900e
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diff --git a/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1/README.md b/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1/README.md
@@ -38,9 +38,11 @@ The purpose of this dataset is to estimate timing and storage requirements for t
 * `esp_subsample_filtered.json`: subset of ESP50k dataset selected for this benchmark
 * `generate-compute.ipynb`: Notebook used to generate the compute expansion `compute.json`
 * `compute.json`: compute expansion specs
-* `generate-compute-wb97xd`: Notebook used to generate the second compute expansion `compute2.json`
+* `generate-compute-wb97xd.ipynb`: Notebook used to generate the second compute expansion `compute2.json`
 * `compute2.json`: second compute expansion specs
 * `ddx_error_exploration.ipynb`: Notebook examining errors in the initial PBE0/def2-TZVPPD/DDX dataset
+* `generate-compute-nodiffuse.ipynb`: Notebook used to generate the third compute expansion `compute3.json`
+* `compute3.json`: Third compute expansion specs, removes diffuse functions
 
 ## Metadata
 * elements: {'H', 'P', 'C', 'N', 'O', 'S', 'Cl', 'I', 'Br', 'F'}
@@ -109,3 +111,35 @@ The purpose of this dataset is to estimate timing and storage requirements for t
 		* mayer_indices
 		* wiberg_lowdin_indices
 		* dipole_polarizabilities
+* Spec: wb97x-d/def2-TZVPP/ddx-water
+  * basis: def2-TZVPP
+  * implicit_solvent: {'ddx_model': 'pcm', 'ddx_radii_scaling': 1.1, 'ddx_radii_set': 'uff', 'ddx_solvent_epsilon': 78.4, 'ddx_solvent': 'water'}
+  * keywords: {'dft_spherical_points': 590, 'dft_radial_points': 99}
+  * maxiter: 200
+  * method: wb97x-d
+  * program: psi4
+  * SCF properties:
+    * dipole
+    * quadrupole
+    * lowdin_charges
+    * mulliken_charges
+    * mbis_charges
+    * mayer_indices
+    * wiberg_lowdin_indices
+    * dipole_polarizabilities
+* Spec: wb97x-d/def2-TZVPP
+  * basis: def2-TZVPP
+  * implicit_solvent: None
+  * keywords: {'dft_spherical_points': 590, 'dft_radial_points': 99}
+  * maxiter: 200
+  * method: wb97x-d
+  * program: psi4
+  * SCF properties:
+    * dipole
+    * quadrupole
+    * lowdin_charges
+    * mulliken_charges
+    * mbis_charges
+    * mayer_indices
+    * wiberg_lowdin_indices
+    * dipole_polarizabilities
diff --git a/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1/compute3.json b/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1/compute3.json
@@ -0,0 +1,81 @@
+{
+  "qc_specifications": {
+    "wb97x-d/def2-TZVPP/ddx-water": {
+      "method": "wb97x-d",
+      "basis": "def2-TZVPP",
+      "program": "psi4",
+      "spec_name": "wb97x-d/def2-TZVPP/ddx-water",
+      "spec_description": "wb97x-d functional with def2-TZVPP basis set and DDX water (eps = 78.4) using UFF radii and 1.1x scaling factor",
+      "store_wavefunction": "none",
+      "implicit_solvent": {
+        "ddx_model": "pcm",
+        "ddx_radii_scaling": 1.1,
+        "ddx_radii_set": "uff",
+        "ddx_solvent_epsilon": 78.4,
+        "ddx_solvent": "water"
+      },
+      "maxiter": 200,
+      "scf_properties": [
+        "dipole",
+        "quadrupole",
+        "lowdin_charges",
+        "mulliken_charges",
+        "mbis_charges",
+        "mayer_indices",
+        "wiberg_lowdin_indices",
+        "dipole_polarizabilities"
+      ],
+      "keywords": {
+        "dft_spherical_points": 590,
+        "dft_radial_points": 99
+      }
+    },
+    "wb97x-d/def2-TZVPP": {
+      "method": "wb97x-d",
+      "basis": "def2-TZVPP",
+      "program": "psi4",
+      "spec_name": "wb97x-d/def2-TZVPP",
+      "spec_description": "wb97x-d functional with def2-TZVPP basis set and vacuum using UFF radii and 1.1x scaling factor",
+      "store_wavefunction": "none",
+      "implicit_solvent": null,
+      "maxiter": 200,
+      "scf_properties": [
+        "dipole",
+        "quadrupole",
+        "lowdin_charges",
+        "mulliken_charges",
+        "mbis_charges",
+        "mayer_indices",
+        "wiberg_lowdin_indices",
+        "dipole_polarizabilities"
+      ],
+      "keywords": {
+        "dft_spherical_points": 590,
+        "dft_radial_points": 99
+      }
+    }
+  },
+  "driver": "properties",
+  "priority": "normal",
+  "dataset_tags": [
+    "openff"
+  ],
+  "compute_tag": "nagl2",
+  "dataset_name": "OpenFF NAGL2 ESP Timing Benchmark v1.1",
+  "dataset_tagline": "wb97x-d/def2-TZVPP single point calculations of ~1000 diverse molecules.",
+  "type": "DataSet",
+  "description": "wb97x-d/def2-TZVPP in vacuum and ddX water single point calculations of ~1000 diverse molecules sub-sampled from the ESP50k, multi-BR ESP, and I fragment datasets, to benchmark computational cost.",
+  "metadata": {
+    "submitter": "amcisaac",
+    "creation_date": "2024-11-04",
+    "collection_type": "DataSet",
+    "dataset_name": "OpenFF NAGL2 ESP Timing Benchmark v1.1",
+    "short_description": "wb97x-d/def2-TZVPP single point calculations of ~1000 diverse molecules.",
+    "long_description_url": "https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1",
+    "long_description": "wb97x-d/def2-TZVPP in vacuum and ddX water single point calculations of ~1000 diverse molecules sub-sampled from the ESP50k, multi-BR ESP, and I fragment datasets, to benchmark computational cost.",
+    "elements": []
+  },
+  "provenance": {},
+  "dataset": {},
+  "filtered_molecules": {}
+}