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#!/bin/bash | ||
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# Create logs directory if it doesn't exist | ||
mkdir -p logs | ||
|
||
jid_list=('JVASP-62940' 'JVASP-20092') | ||
# Define arrays of JIDs and calculators | ||
#jid_list=('JVASP-1002' 'JVASP-890' 'JVASP-39' 'JVASP-30' 'JVASP-62940' 'JVASP-20092' 'JVASP-8003' 'JVASP-1192' 'JVASP-23' 'JVASP-1195' 'JVASP-96' 'JVASP-10591' 'JVASP-1198' 'JVASP-1312' 'JVASP-133719' 'JVASP-36873' 'JVASP-1327' 'JVASP-1372' 'JVASP-1408' 'JVASP-8184' 'JVASP-1174' 'JVASP-1177' 'JVASP-1180' 'JVASP-1183' 'JVASP-1186' 'JVASP-1189' 'JVASP-91' 'JVASP-8158' 'JVASP-8118' 'JVASP-107' 'JVASP-36018' 'JVASP-36408' 'JVASP-105410' 'JVASP-36403' 'JVASP-1008' 'JVASP-95268' 'JVASP-21211' 'JVASP-1023' 'JVASP-7836' 'JVASP-9166' 'JVASP-1201' 'JVASP-85478' 'JVASP-1115' 'JVASP-1112' 'JVASP-1103' 'JVASP-1109' 'JVASP-131' 'JVASP-149916' 'JVASP-111005' 'JVASP-25' 'JVASP-1067' 'JVASP-154954' 'JVASP-59712' 'JVASP-10703' 'JVASP-1213' 'JVASP-19007' 'JVASP-10114' 'JVASP-9175' 'JVASP-104' 'JVASP-10036' 'JVASP-18983' 'JVASP-1216' 'JVASP-79522' 'JVASP-1222' 'JVASP-10037' 'JVASP-110' 'JVASP-8082' 'JVASP-1240' 'JVASP-51480' 'JVASP-29539' 'JVASP-54' 'JVASP-29556' 'JVASP-1915' 'JVASP-75662' 'JVASP-101764' 'JVASP-22694' 'JVASP-4282' 'JVASP-76195' 'JVASP-8554' 'JVASP-149871' 'JVASP-2376' 'JVASP-14163' 'JVASP-26248' 'JVASP-18942' 'JVASP-3510' 'JVASP-5224' 'JVASP-8559' 'JVASP-85416' 'JVASP-9117' 'JVASP-90668' 'JVASP-10689' 'JVASP-106381' 'JVASP-108773' 'JVASP-101184' 'JVASP-103127' 'JVASP-104764' 'JVASP-102336' 'JVASP-110231' 'JVASP-108770' 'JVASP-101074' 'JVASP-149906' 'JVASP-99732' 'JVASP-106686' 'JVASP-110952' 'JVASP-106363' 'JVASP-972' 'JVASP-825' 'JVASP-813' 'JVASP-816' 'JVASP-802' 'JVASP-1029' 'JVASP-861' 'JVASP-943' 'JVASP-963' 'JVASP-14616' 'JVASP-867' 'JVASP-14968' 'JVASP-14970' 'JVASP-19780' 'JVASP-9147' 'JVASP-34249' 'JVASP-43367' 'JVASP-113' 'JVASP-41' 'JVASP-58349' 'JVASP-34674' 'JVASP-34656' 'JVASP-34249' 'JVASP-32') | ||
calculator_types=("alignn_ff_12_2_24") | ||
|
||
# Loop through each JID and calculator combination | ||
for jid in "${jid_list[@]}"; do | ||
for calculator in "${calculator_types[@]}"; do | ||
|
||
# Submit each job with a separate sbatch command, requesting a dedicated node | ||
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" | ||
], | ||
"bulk_relaxation_settings": { | ||
"filter_type": "ExpCellFilter", | ||
"relaxation_settings": { | ||
"fmax": 0.05, | ||
"steps": 200, | ||
"constant_volume": false | ||
} | ||
}, | ||
"calculator_settings": { | ||
"matgl": { | ||
"model": "M3GNet-MP-2021.2.8-PES" | ||
}, | ||
"alignn_ff": { | ||
"stress_weight": 0.3 | ||
}, | ||
"chgnet": {} | ||
}, | ||
"phonon_settings": { | ||
"dim": [2, 2, 2], | ||
"distance": 0.2 | ||
}, | ||
"use_conventional_cell": false, | ||
"surface_settings": { | ||
"indices_list": [ | ||
[1, 0, 0], | ||
[1, 1, 1], | ||
[1, 1, 0], | ||
[0, 1, 1], | ||
[0, 0, 1], | ||
[0, 1, 0] | ||
], | ||
"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 | ||
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||
done | ||
done |
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#!/bin/bash | ||
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# Create logs directory if it doesn't exist | ||
mkdir -p logs | ||
|
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jid_list=('JVASP-62940' 'JVASP-20092') | ||
# Define arrays of JIDs and calculators | ||
#jid_list=('JVASP-1002' 'JVASP-890' 'JVASP-39' 'JVASP-30' 'JVASP-62940' 'JVASP-20092' 'JVASP-8003' 'JVASP-1192' 'JVASP-23' 'JVASP-1195' 'JVASP-96' 'JVASP-10591' 'JVASP-1198' 'JVASP-1312' 'JVASP-133719' 'JVASP-36873' 'JVASP-1327' 'JVASP-1372' 'JVASP-1408' 'JVASP-8184' 'JVASP-1174' 'JVASP-1177' 'JVASP-1180' 'JVASP-1183' 'JVASP-1186' 'JVASP-1189' 'JVASP-91' 'JVASP-8158' 'JVASP-8118' 'JVASP-107' 'JVASP-36018' 'JVASP-36408' 'JVASP-105410' 'JVASP-36403' 'JVASP-1008' 'JVASP-95268' 'JVASP-21211' 'JVASP-1023' 'JVASP-7836' 'JVASP-9166' 'JVASP-1201' 'JVASP-85478' 'JVASP-1115' 'JVASP-1112' 'JVASP-1103' 'JVASP-1109' 'JVASP-131' 'JVASP-149916' 'JVASP-111005' 'JVASP-25' 'JVASP-1067' 'JVASP-154954' 'JVASP-59712' 'JVASP-10703' 'JVASP-1213' 'JVASP-19007' 'JVASP-10114' 'JVASP-9175' 'JVASP-104' 'JVASP-10036' 'JVASP-18983' 'JVASP-1216' 'JVASP-79522' 'JVASP-1222' 'JVASP-10037' 'JVASP-110' 'JVASP-8082' 'JVASP-1240' 'JVASP-51480' 'JVASP-29539' 'JVASP-54' 'JVASP-29556' 'JVASP-1915' 'JVASP-75662' 'JVASP-101764' 'JVASP-22694' 'JVASP-4282' 'JVASP-76195' 'JVASP-8554' 'JVASP-149871' 'JVASP-2376' 'JVASP-14163' 'JVASP-26248' 'JVASP-18942' 'JVASP-3510' 'JVASP-5224' 'JVASP-8559' 'JVASP-85416' 'JVASP-9117' 'JVASP-90668' 'JVASP-10689' 'JVASP-106381' 'JVASP-108773' 'JVASP-101184' 'JVASP-103127' 'JVASP-104764' 'JVASP-102336' 'JVASP-110231' 'JVASP-108770' 'JVASP-101074' 'JVASP-149906' 'JVASP-99732' 'JVASP-106686' 'JVASP-110952' 'JVASP-106363' 'JVASP-972' 'JVASP-825' 'JVASP-813' 'JVASP-816' 'JVASP-802' 'JVASP-1029' 'JVASP-861' 'JVASP-943' 'JVASP-963' 'JVASP-14616' 'JVASP-867' 'JVASP-14968' 'JVASP-14970' 'JVASP-19780' 'JVASP-9147' 'JVASP-34249' 'JVASP-43367' 'JVASP-113' 'JVASP-41' 'JVASP-58349' 'JVASP-34674' 'JVASP-34656' 'JVASP-34249' 'JVASP-32') | ||
calculator_types=("alignn_ff_12_2_24") | ||
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||
# Loop through each JID and calculator combination | ||
for jid in "${jid_list[@]}"; do | ||
for calculator in "${calculator_types[@]}"; do | ||
|
||
# Submit each job with a separate sbatch command, requesting a dedicated node | ||
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" | ||
], | ||
"bulk_relaxation_settings": { | ||
"filter_type": "ExpCellFilter", | ||
"relaxation_settings": { | ||
"fmax": 0.05, | ||
"steps": 200, | ||
"constant_volume": false | ||
} | ||
}, | ||
"calculator_settings": { | ||
"matgl": { | ||
"model": "M3GNet-MP-2021.2.8-PES" | ||
}, | ||
"alignn_ff": { | ||
"stress_weight": 0.3 | ||
}, | ||
"chgnet": {} | ||
}, | ||
"phonon_settings": { | ||
"dim": [2, 2, 2], | ||
"distance": 0.2 | ||
}, | ||
"use_conventional_cell": false, | ||
"surface_settings": { | ||
"indices_list": [ | ||
[1, 0, 0], | ||
[1, 1, 1], | ||
[1, 1, 0], | ||
[0, 1, 1], | ||
[0, 0, 1], | ||
[0, 1, 0] | ||
], | ||
"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 | ||
|
||
done | ||
done |
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{ | ||
"calculator_type": "alignn_ff_12_2_24", | ||
"mlearn_elements": [ | ||
"Cu" | ||
], | ||
"forces_mae_Cu": 0.21592027727012433, | ||
"stresses_mae_Cu": 2.2145441603034666 | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,39 @@ | ||
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' |
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{ | ||
"calculator_type": "alignn_ff_12_2_24", | ||
"mlearn_elements": [ | ||
"Ge" | ||
], | ||
"forces_mae_Ge": 0.3953967136776566, | ||
"stresses_mae_Ge": 0.780313668468333 | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,35 @@ | ||
2024-12-03 16:35:00,317 - INFO - Filtered dataset to 253 entries containing element 'Ge' | ||
2024-12-03 16:35:06,862 - INFO - Processed 1/253 structures. | ||
2024-12-03 16:35:07,930 - INFO - Processed 11/253 structures. | ||
2024-12-03 16:35:08,922 - INFO - Processed 21/253 structures. | ||
2024-12-03 16:35:09,918 - INFO - Processed 31/253 structures. | ||
2024-12-03 16:35:11,485 - INFO - Processed 41/253 structures. | ||
2024-12-03 16:35:13,671 - INFO - Processed 51/253 structures. | ||
2024-12-03 16:35:15,302 - INFO - Processed 61/253 structures. | ||
2024-12-03 16:35:16,906 - INFO - Processed 71/253 structures. | ||
2024-12-03 16:35:18,436 - INFO - Processed 81/253 structures. | ||
2024-12-03 16:35:20,031 - INFO - Processed 91/253 structures. | ||
2024-12-03 16:35:21,609 - INFO - Processed 101/253 structures. | ||
2024-12-03 16:35:23,173 - INFO - Processed 111/253 structures. | ||
2024-12-03 16:35:24,746 - INFO - Processed 121/253 structures. | ||
2024-12-03 16:35:26,216 - INFO - Processed 131/253 structures. | ||
2024-12-03 16:35:27,865 - INFO - Processed 141/253 structures. | ||
2024-12-03 16:35:29,462 - INFO - Processed 151/253 structures. | ||
2024-12-03 16:35:31,006 - INFO - Processed 161/253 structures. | ||
2024-12-03 16:35:31,747 - INFO - Processed 171/253 structures. | ||
2024-12-03 16:35:32,898 - INFO - Processed 181/253 structures. | ||
2024-12-03 16:35:34,102 - INFO - Processed 191/253 structures. | ||
2024-12-03 16:35:35,310 - INFO - Processed 201/253 structures. | ||
2024-12-03 16:35:36,190 - INFO - Processed 211/253 structures. | ||
2024-12-03 16:35:37,106 - INFO - Processed 221/253 structures. | ||
2024-12-03 16:35:38,029 - INFO - Processed 231/253 structures. | ||
2024-12-03 16:35:39,439 - INFO - Processed 241/253 structures. | ||
2024-12-03 16:35:41,176 - INFO - Processed 251/253 structures. | ||
2024-12-03 16:35:41,413 - INFO - Saved force comparison data to 'mlearn_analysis_Ge_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Ge-test-multimae.csv' | ||
2024-12-03 16:35:41,420 - INFO - Saved stress comparison data to 'mlearn_analysis_Ge_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Ge-test-multimae.csv' | ||
2024-12-03 16:35:41,548 - INFO - Zipped data to 'mlearn_analysis_Ge_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Ge-test-multimae.csv.zip' | ||
2024-12-03 16:35:41,559 - INFO - Zipped data to 'mlearn_analysis_Ge_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Ge-test-multimae.csv.zip' | ||
2024-12-03 16:35:41,586 - INFO - Forces MAE for element 'Ge': 0.395397 eV/Å | ||
2024-12-03 16:35:41,591 - INFO - Stresses MAE for element 'Ge': 0.780314 GPa | ||
2024-12-03 16:35:44,299 - INFO - Saved parity plot for Forces as 'mlearn_analysis_Ge_alignn_ff_12_2_24/forces_parity_plot_Ge.png' | ||
2024-12-03 16:35:45,337 - INFO - Saved parity plot for Stresses as 'mlearn_analysis_Ge_alignn_ff_12_2_24/stresses_parity_plot_Ge.png' |
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{ | ||
"calculator_type": "alignn_ff_12_2_24", | ||
"mlearn_elements": [ | ||
"Li" | ||
], | ||
"forces_mae_Li": 0.12188066042696061, | ||
"stresses_mae_Li": 0.43449990685579476 | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,36 @@ | ||
2024-12-03 16:34:59,871 - INFO - Filtered dataset to 270 entries containing element 'Li' | ||
2024-12-03 16:35:07,046 - INFO - Processed 1/270 structures. | ||
2024-12-03 16:35:10,326 - INFO - Processed 11/270 structures. | ||
2024-12-03 16:35:13,532 - INFO - Processed 21/270 structures. | ||
2024-12-03 16:35:16,781 - INFO - Processed 31/270 structures. | ||
2024-12-03 16:35:20,042 - INFO - Processed 41/270 structures. | ||
2024-12-03 16:35:23,305 - INFO - Processed 51/270 structures. | ||
2024-12-03 16:35:26,229 - INFO - Processed 61/270 structures. | ||
2024-12-03 16:35:29,758 - INFO - Processed 71/270 structures. | ||
2024-12-03 16:35:33,174 - INFO - Processed 81/270 structures. | ||
2024-12-03 16:35:36,574 - INFO - Processed 91/270 structures. | ||
2024-12-03 16:35:40,080 - INFO - Processed 101/270 structures. | ||
2024-12-03 16:35:43,827 - INFO - Processed 111/270 structures. | ||
2024-12-03 16:35:47,521 - INFO - Processed 121/270 structures. | ||
2024-12-03 16:35:51,043 - INFO - Processed 131/270 structures. | ||
2024-12-03 16:35:54,665 - INFO - Processed 141/270 structures. | ||
2024-12-03 16:35:58,204 - INFO - Processed 151/270 structures. | ||
2024-12-03 16:36:01,798 - INFO - Processed 161/270 structures. | ||
2024-12-03 16:36:05,497 - INFO - Processed 171/270 structures. | ||
2024-12-03 16:36:09,432 - INFO - Processed 181/270 structures. | ||
2024-12-03 16:36:13,116 - INFO - Processed 191/270 structures. | ||
2024-12-03 16:36:16,916 - INFO - Processed 201/270 structures. | ||
2024-12-03 16:36:19,962 - INFO - Processed 211/270 structures. | ||
2024-12-03 16:36:21,998 - INFO - Processed 221/270 structures. | ||
2024-12-03 16:36:22,667 - INFO - Processed 231/270 structures. | ||
2024-12-03 16:36:23,333 - INFO - Processed 241/270 structures. | ||
2024-12-03 16:36:26,637 - INFO - Processed 251/270 structures. | ||
2024-12-03 16:36:29,621 - INFO - Processed 261/270 structures. | ||
2024-12-03 16:36:31,318 - INFO - Saved force comparison data to 'mlearn_analysis_Li_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Li-test-multimae.csv' | ||
2024-12-03 16:36:31,327 - INFO - Saved stress comparison data to 'mlearn_analysis_Li_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Li-test-multimae.csv' | ||
2024-12-03 16:36:31,472 - INFO - Zipped data to 'mlearn_analysis_Li_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Li-test-multimae.csv.zip' | ||
2024-12-03 16:36:31,485 - INFO - Zipped data to 'mlearn_analysis_Li_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Li-test-multimae.csv.zip' | ||
2024-12-03 16:36:31,520 - INFO - Forces MAE for element 'Li': 0.121881 eV/Å | ||
2024-12-03 16:36:31,528 - INFO - Stresses MAE for element 'Li': 0.434500 GPa | ||
2024-12-03 16:36:33,844 - INFO - Saved parity plot for Forces as 'mlearn_analysis_Li_alignn_ff_12_2_24/forces_parity_plot_Li.png' | ||
2024-12-03 16:36:34,834 - INFO - Saved parity plot for Stresses as 'mlearn_analysis_Li_alignn_ff_12_2_24/stresses_parity_plot_Li.png' |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 | ||
|
Large diffs are not rendered by default.
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,15 @@ | ||
{ | ||
"model_name": "CHIPS-FF", | ||
"project_url": "https://github.com/usnistgov/chipsff", | ||
"date_submitted": "11-22-2024", | ||
"author_email": "daniel.wines@nist.gov", | ||
"time_taken_seconds": {}, | ||
"team_name": "JARVIS", | ||
"language": "python", | ||
"os": "linux", | ||
"software_used": "jarvis-tools,numpy,scipy,torch,alignn", | ||
"hardware_used": "mr-french at NIST", | ||
"git_url": [ | ||
"https://github.com/usnistgov/chipsff" | ||
] | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,8 @@ | ||
{ | ||
"calculator_type": "alignn_ff_12_2_24", | ||
"mlearn_elements": [ | ||
"Mo" | ||
], | ||
"forces_mae_Mo": 0.8687823188310289, | ||
"stresses_mae_Mo": 5.529467208325023 | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,31 @@ | ||
2024-12-03 16:35:08,320 - INFO - Filtered dataset to 217 entries containing element 'Mo' | ||
2024-12-03 16:35:09,997 - INFO - Processed 1/217 structures. | ||
2024-12-03 16:35:15,335 - INFO - Processed 11/217 structures. | ||
2024-12-03 16:35:21,398 - INFO - Processed 21/217 structures. | ||
2024-12-03 16:35:27,153 - INFO - Processed 31/217 structures. | ||
2024-12-03 16:35:32,823 - INFO - Processed 41/217 structures. | ||
2024-12-03 16:35:38,458 - INFO - Processed 51/217 structures. | ||
2024-12-03 16:35:44,255 - INFO - Processed 61/217 structures. | ||
2024-12-03 16:35:50,052 - INFO - Processed 71/217 structures. | ||
2024-12-03 16:35:56,290 - INFO - Processed 81/217 structures. | ||
2024-12-03 16:36:02,325 - INFO - Processed 91/217 structures. | ||
2024-12-03 16:36:09,036 - INFO - Processed 101/217 structures. | ||
2024-12-03 16:36:15,920 - INFO - Processed 111/217 structures. | ||
2024-12-03 16:36:22,901 - INFO - Processed 121/217 structures. | ||
2024-12-03 16:36:28,847 - INFO - Processed 131/217 structures. | ||
2024-12-03 16:36:32,234 - INFO - Processed 141/217 structures. | ||
2024-12-03 16:36:37,249 - INFO - Processed 151/217 structures. | ||
2024-12-03 16:36:41,447 - INFO - Processed 161/217 structures. | ||
2024-12-03 16:36:45,940 - INFO - Processed 171/217 structures. | ||
2024-12-03 16:36:49,978 - INFO - Processed 181/217 structures. | ||
2024-12-03 16:36:54,062 - INFO - Processed 191/217 structures. | ||
2024-12-03 16:36:58,221 - INFO - Processed 201/217 structures. | ||
2024-12-03 16:37:01,613 - INFO - Processed 211/217 structures. | ||
2024-12-03 16:37:04,120 - INFO - Saved force comparison data to 'mlearn_analysis_Mo_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Mo-test-multimae.csv' | ||
2024-12-03 16:37:04,128 - INFO - Saved stress comparison data to 'mlearn_analysis_Mo_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Mo-test-multimae.csv' | ||
2024-12-03 16:37:04,366 - INFO - Zipped data to 'mlearn_analysis_Mo_alignn_ff_12_2_24/AI-MLFF-forces-mlearn_Mo-test-multimae.csv.zip' | ||
2024-12-03 16:37:04,379 - INFO - Zipped data to 'mlearn_analysis_Mo_alignn_ff_12_2_24/AI-MLFF-stresses-mlearn_Mo-test-multimae.csv.zip' | ||
2024-12-03 16:37:04,454 - INFO - Forces MAE for element 'Mo': 0.868782 eV/Å | ||
2024-12-03 16:37:04,471 - INFO - Stresses MAE for element 'Mo': 5.529467 GPa | ||
2024-12-03 16:37:07,572 - INFO - Saved parity plot for Forces as 'mlearn_analysis_Mo_alignn_ff_12_2_24/forces_parity_plot_Mo.png' | ||
2024-12-03 16:37:09,274 - INFO - Saved parity plot for Stresses as 'mlearn_analysis_Mo_alignn_ff_12_2_24/stresses_parity_plot_Mo.png' |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 | ||
|