Merge pull request #344 from wines1/main

Adding updated chipsff benchmarks

jarvis_leaderboard/contributions/mlearn_analysis_Cu_alignn_ff_12_2_24/mlearn_alignn_ff_12_2_24_job_info.json

@@ -0,0 +1,8 @@
+{
+    "calculator_type": "alignn_ff_12_2_24",
+    "mlearn_elements": [
+        "Cu"
+    ],
+    "forces_mae_Cu": 0.21592027727012433,
+    "stresses_mae_Cu": 2.2145441603034666
+}

jarvis_leaderboard/contributions/mlearn_analysis_Cu_alignn_ff_12_2_24/mlearn_analysis_log.txt

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+2024-12-03 16:35:00,376 - INFO - Filtered dataset to 293 entries containing element 'Cu'
+2024-12-03 16:35:07,397 - INFO - Processed 1/293 structures.
+2024-12-03 16:35:15,377 - INFO - Processed 11/293 structures.
+2024-12-03 16:35:23,369 - INFO - Processed 21/293 structures.
+2024-12-03 16:35:31,167 - INFO - Processed 31/293 structures.
+2024-12-03 16:35:35,574 - INFO - Processed 41/293 structures.
+2024-12-03 16:35:40,962 - INFO - Processed 51/293 structures.
+2024-12-03 16:35:47,479 - INFO - Processed 61/293 structures.
+2024-12-03 16:35:54,676 - INFO - Processed 71/293 structures.
+2024-12-03 16:36:01,255 - INFO - Processed 81/293 structures.
+2024-12-03 16:36:08,268 - INFO - Processed 91/293 structures.
+2024-12-03 16:36:14,984 - INFO - Processed 101/293 structures.
+2024-12-03 16:36:22,058 - INFO - Processed 111/293 structures.
+2024-12-03 16:36:28,342 - INFO - Processed 121/293 structures.
+2024-12-03 16:36:34,290 - INFO - Processed 131/293 structures.
+2024-12-03 16:36:40,901 - INFO - Processed 141/293 structures.
+2024-12-03 16:36:47,653 - INFO - Processed 151/293 structures.
+2024-12-03 16:36:53,432 - INFO - Processed 161/293 structures.
+2024-12-03 16:36:59,260 - INFO - Processed 171/293 structures.
+2024-12-03 16:37:05,451 - INFO - Processed 181/293 structures.
+2024-12-03 16:37:10,698 - INFO - Processed 191/293 structures.
+2024-12-03 16:37:15,898 - INFO - Processed 201/293 structures.
+2024-12-03 16:37:20,620 - INFO - Processed 211/293 structures.
+2024-12-03 16:37:25,270 - INFO - Processed 221/293 structures.
+2024-12-03 16:37:29,780 - INFO - Processed 231/293 structures.
+2024-12-03 16:37:35,096 - INFO - Processed 241/293 structures.
+2024-12-03 16:37:40,850 - INFO - Processed 251/293 structures.
+2024-12-03 16:37:46,341 - INFO - Processed 261/293 structures.
+2024-12-03 16:37:51,072 - INFO - Processed 271/293 structures.
+2024-12-03 16:37:56,916 - INFO - Processed 281/293 structures.
+2024-12-03 16:38:02,651 - INFO - Processed 291/293 structures.
+2024-12-03 16:38:03,955 - INFO - Saved force comparison data to 'mlearn_analysis_Cu_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Cu-test-multimae.csv'
+2024-12-03 16:38:03,961 - INFO - Saved stress comparison data to 'mlearn_analysis_Cu_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Cu-test-multimae.csv'
+2024-12-03 16:38:04,209 - INFO - Zipped data to 'mlearn_analysis_Cu_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Cu-test-multimae.csv.zip'
+2024-12-03 16:38:04,219 - INFO - Zipped data to 'mlearn_analysis_Cu_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Cu-test-multimae.csv.zip'
+2024-12-03 16:38:04,264 - INFO - Forces MAE for element 'Cu': 0.215920 eV/Å
+2024-12-03 16:38:04,269 - INFO - Stresses MAE for element 'Cu': 2.214544 GPa
+2024-12-03 16:38:07,828 - INFO - Saved parity plot for Forces as 'mlearn_analysis_Cu_alignn_ff_12_2_24/forces_parity_plot_Cu.png'
+2024-12-03 16:38:08,554 - INFO - Saved parity plot for Stresses as 'mlearn_analysis_Cu_alignn_ff_12_2_24/stresses_parity_plot_Cu.png'

jarvis_leaderboard/contributions/mlearn_analysis_Cu_alignn_ff_12_2_24/run.sh

@@ -0,0 +1,148 @@
+#!/bin/bash
+
+# Create logs directory if it doesn't exist
+mkdir -p logs
+
+# Define arrays of JIDs, calculators, and mlearn elements
+calculator_types=("alignn_ff_12_2_24")
+mlearn_elements=("Si" "Ge" "Cu" "Ni" "Li" "Mo")
+
+# Function to submit a job for bulk material calculations
+submit_bulk_job() {
+  local jid=$1
+  local calculator=$2
+
+  sbatch <<EOT
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=16
+#SBATCH --time=30-00:00:00
+#SBATCH --partition=rack1,rack2e,rack3,rack4,rack4e,rack5,rack6
+#SBATCH --job-name=${jid}_${calculator}
+#SBATCH --output=logs/${jid}_${calculator}_%j.out
+#SBATCH --error=logs/${jid}_${calculator}_%j.err
+
+# Generate input JSON file for this combination
+cat > input_${jid}_${calculator}.json <<JSON
+{
+  "jid": "$jid",
+  "calculator_type": "$calculator",
+  "chemical_potentials_file": "chemical_potentials.json",
+  "properties_to_calculate": [
+    "relax_structure",
+    "calculate_ev_curve",
+    "calculate_formation_energy",
+    "calculate_elastic_tensor",
+    "run_phonon_analysis",
+    "analyze_surfaces",
+    "analyze_defects",
+    "run_phonon3_analysis",
+    "general_melter",
+    "calculate_rdf"
+  ],
+  "bulk_relaxation_settings": {
+    "filter_type": "ExpCellFilter",
+    "relaxation_settings": {
+      "fmax": 0.05,
+      "steps": 200,
+      "constant_volume": false
+    }
+  },
+  "phonon_settings": {
+    "dim": [2, 2, 2],
+    "distance": 0.2
+  },
+  "use_conventional_cell": true,
+  "surface_settings": {
+    "indices_list": [
+      [0, 1, 0],
+      [0, 0, 1]
+    ],
+    "layers": 4,
+    "vacuum": 18,
+    "relaxation_settings": {
+      "fmax": 0.05,
+      "steps": 200,
+      "constant_volume": true
+    },
+    "filter_type": "ExpCellFilter"
+  },
+  "defect_settings": {
+    "generate_settings": {
+      "on_conventional_cell": true,
+      "enforce_c_size": 8,
+      "extend": 1
+    },
+    "relaxation_settings": {
+      "fmax": 0.05,
+      "steps": 200,
+      "constant_volume": true
+    },
+    "filter_type": "ExpCellFilter"
+  },
+  "phonon3_settings": {
+    "dim": [2, 2, 2],
+    "distance": 0.2
+  },
+  "md_settings": {
+    "dt": 1,
+    "temp0": 35,
+    "nsteps0": 10,
+    "temp1": 200,
+    "nsteps1": 20,
+    "taut": 20,
+    "min_size": 10.0
+  }
+}
+JSON
+
+# Run the Python analysis for this JID/calculator combination
+python run_chipsff.py --input_file input_${jid}_${calculator}.json
+
+EOT
+}
+
+# Function to submit a job for mlearn analysis
+submit_mlearn_job() {
+  local element=$1
+  local calculator=$2
+
+  sbatch <<EOT
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=16
+#SBATCH --time=1-00:00:00
+#SBATCH --partition=rack1,rack2e,rack3,rack4,rack4e,rack5,rack6
+#SBATCH --job-name=mlearn_${element}_${calculator}
+#SBATCH --output=logs/mlearn_${element}_${calculator}_%j.out
+#SBATCH --error=logs/mlearn_${element}_${calculator}_%j.err
+
+# Generate input JSON file for this mlearn element/calculator combination
+cat > input_mlearn_${element}_${calculator}.json <<JSON
+{
+  "mlearn_elements": ["$element"],
+  "calculator_type": "$calculator",
+  "properties_to_calculate": ["compare_mlearn_forces"]
+}
+JSON
+
+# Run the Python analysis for this mlearn element/calculator combination
+python run_chipsff.py --input_file input_mlearn_${element}_${calculator}.json
+
+EOT
+}
+
+# Loop through each JID and calculator combination for bulk calculations
+for jid in "${jid_list[@]}"; do
+  for calculator in "${calculator_types[@]}"; do
+    submit_bulk_job "$jid" "$calculator"
+  done
+done
+
+# Loop through each mlearn element and calculator combination for mlearn analysis
+for element in "${mlearn_elements[@]}"; do
+  for calculator in "${calculator_types[@]}"; do
+    submit_mlearn_job "$element" "$calculator"
+  done
+done
+