diff --git a/dvc.lock b/dvc.lock index 78c792b..2cd1d89 100644 --- a/dvc.lock +++ b/dvc.lock @@ -21337,3 +21337,253 @@ stages: hash: md5 md5: 0a366e37c5368c0f3d9888f5d26a5d13 size: 58176 + AIMD_ConfigurationSelection: + cmd: zntrack run ipsuite.nodes.IndexSelection --name AIMD_ConfigurationSelection + deps: + - path: nodes/classical/AddData/atoms.h5 + hash: md5 + md5: 4b28c7c0a6ae386fce15e8c814259378 + size: 19874075 + - path: nodes/classical/AddData/node-meta.json + hash: md5 + md5: e875cc934db72ea4d2b9d3be558e88d1 + size: 48 + params: + params.yaml: + AIMD_ConfigurationSelection: + indices: + - 2000 + outs: + - path: nodes/AIMD/ConfigurationSelection/node-meta.json + hash: md5 + md5: da71f5aa940cb81b46f4aea6f433b722 + size: 48 + - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json + hash: md5 + md5: 755d6c816224dec168bb7ef675f0733d + size: 49 + - path: nodes/AIMD/ConfigurationSelection/selection.png + hash: md5 + md5: 509cc04ed4e1e293ee81eb67105a6454 + size: 25192 + AIMD_CP2KSinglePoint: + cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name AIMD_CP2KSinglePoint + deps: + - path: GTH_BASIS_SETS + hash: md5 + md5: 518e733a7344699cf0b4192bb97eb6a3 + size: 119403 + - path: GTH_POTENTIALS + hash: md5 + md5: 3a35b03b26b8ba5cf6c1d849dba11f15 + size: 128982 + - path: dftd3.dat + hash: md5 + md5: 88745bcc951a4bcdccc4d6bcfa78d105 + size: 1959318 + - path: nodes/AIMD/ConfigurationSelection/node-meta.json + hash: md5 + md5: da71f5aa940cb81b46f4aea6f433b722 + size: 48 + - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json + hash: md5 + md5: 755d6c816224dec168bb7ef675f0733d + size: 49 + - path: nodes/AIMD/ConfigurationSelection/selection.png + hash: md5 + md5: 509cc04ed4e1e293ee81eb67105a6454 + size: 25192 + params: + config/cp2k.yaml: + force_eval: + method: quickstep + DFT: + mgrid: + cutoff: 800 + rel_cutoff: 60 + ngrids: 5 + QS: + eps_filter_matrix: 0.0 + eps_pgf_orb: 0.0001 + SCF: + scf_guess: restart + max_scf: 100 + eps_scf: 1e-06 + OT: + minimizer: diis + preconditioner: full_single_inverse + outer_scf: + max_scf: 100 + eps_scf: 1e-06 + print: + restart: + each: + QS_SCF: 0 + XC: + xc_functional: + becke97: + parametrization: B97-3c + scale_c: 1.0 + scale_x: 1.0 + vdw_potential: + pair_potential: + type: dftd3(bj) + parameter_file_name: dftd3.dat + reference_functional: B97-3c + r_cutoff: 7.93766 + calculate_c9_term: true + short_range_correction: true + potential_type: pair_potential + charge: 0 + basis_set_file_name: GTH_BASIS_SETS + potential_file_name: GTH_POTENTIALS + subsys: + kind: + N: + basis_set: TZVP-GTH-q5 + potential: GTH-PBE-q5 + C: + basis_set: TZVP-GTH-q4 + potential: GTH-PBE-q4 + H: + basis_set: TZVP-GTH-q1 + potential: GTH-PBE-q1 + B: + basis_set: TZVP-GTH-q3 + potential: GTH-PBE-q3 + F: + basis_set: TZVP-GTH-q7 + potential: GTH-PBE-q7 + outs: + - path: nodes/AIMD/CP2KSinglePoint/atoms.h5 + hash: md5 + md5: 913b91fba4bf2e86ee5fc84efeb73667 + size: 57448 + - path: nodes/AIMD/CP2KSinglePoint/cp2k + hash: md5 + md5: 97c3ffe7efca455b49b387f6ceb24389.dir + size: 12384695 + nfiles: 3 + - path: nodes/AIMD/CP2KSinglePoint/node-meta.json + hash: md5 + md5: a61c58e291a27dd324ab6bb3b1ac6c68 + size: 48 + AIMD_ASEMD: + cmd: zntrack run ipsuite.nodes.ASEMD --name AIMD_ASEMD + deps: + - path: nodes/AIMD/CP2KSinglePoint/atoms.h5 + hash: md5 + md5: 913b91fba4bf2e86ee5fc84efeb73667 + size: 57448 + - path: nodes/AIMD/CP2KSinglePoint/cp2k + hash: md5 + md5: 97c3ffe7efca455b49b387f6ceb24389.dir + size: 12384695 + nfiles: 3 + - path: nodes/AIMD/CP2KSinglePoint/node-meta.json + hash: md5 + md5: a61c58e291a27dd324ab6bb3b1ac6c68 + size: 48 + - path: nodes/AIMD/ConfigurationSelection/node-meta.json + hash: md5 + md5: da71f5aa940cb81b46f4aea6f433b722 + size: 48 + - path: nodes/AIMD/ConfigurationSelection/selected_configurations.json + hash: md5 + md5: 755d6c816224dec168bb7ef675f0733d + size: 49 + - path: nodes/AIMD/ConfigurationSelection/selection.png + hash: md5 + md5: 509cc04ed4e1e293ee81eb67105a6454 + size: 25192 + params: + params.yaml: + AIMD_ASEMD: + data_id: -1 + dump_rate: 100 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 1 + seed: 42 + steps: 13200 + use_momenta: false + wrap: false + AIMD_ASEMD+thermostat: + pfactor: 54.27299976036698 + pressure: 6.324209121801211e-07 + temperature: 303 + tetragonal_strain: true + time_step: 0.5 + ttime: 2.455673697116016 + outs: + - path: nodes/AIMD/ASEMD/metrics_dict.csv + hash: md5 + md5: 39783ea5f81cfba41bef335289076ff8 + size: 22 + - path: nodes/AIMD/ASEMD/model + hash: md5 + md5: b8aa27ddf15af66ef17364db5dc35728.dir + size: 894284091 + nfiles: 7 + - path: nodes/AIMD/ASEMD/node-meta.json + hash: md5 + md5: 54c35749a37173d453737baac1923f63 + size: 48 + - path: nodes/AIMD/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/AIMD/ASEMD/trajectory.h5 + hash: md5 + md5: 670ca00ab2a35c9f28d23a62532cb6e0 + size: 319839264 + AIMD_AnalyseDensity: + cmd: zntrack run ipsuite.nodes.AnalyseDensity --name AIMD_AnalyseDensity + deps: + - path: nodes/AIMD/ASEMD/metrics_dict.csv + hash: md5 + md5: 39783ea5f81cfba41bef335289076ff8 + size: 22 + - path: nodes/AIMD/ASEMD/model + hash: md5 + md5: b8aa27ddf15af66ef17364db5dc35728.dir + size: 894284091 + nfiles: 7 + - path: nodes/AIMD/ASEMD/node-meta.json + hash: md5 + md5: 54c35749a37173d453737baac1923f63 + size: 48 + - path: nodes/AIMD/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/AIMD/ASEMD/trajectory.h5 + hash: md5 + md5: 670ca00ab2a35c9f28d23a62532cb6e0 + size: 319839264 + params: + params.yaml: + AIMD_AnalyseDensity: + end: + start: 0 + window: 1000 + outs: + - path: nodes/AIMD/AnalyseDensity/density.json + hash: md5 + md5: 489aff3c573200e5fce6489ef42df802 + size: 66 + - path: nodes/AIMD/AnalyseDensity/density.png + hash: md5 + md5: 08764b82caac0c44a0ea410fc57f085f + size: 39294 + - path: nodes/AIMD/AnalyseDensity/node-meta.json + hash: md5 + md5: 34b6390ccd61b45d74f4c8a1fb686800 + size: 48 + - path: nodes/AIMD/AnalyseDensity/results.csv + hash: md5 + md5: d225a5b9350de6b87baaea07e4c80719 + size: 315610 diff --git a/dvc.yaml b/dvc.yaml index f89d065..a475c1e 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -179,7 +179,79 @@ plots: x_label: epochs y: val_loss y_label: validation loss +- nodes/AIMD/ASEMD/metrics_dict.csv: {} +- nodes/AIMD/AnalyseDensity/density.png: {} +- nodes/AIMD/AnalyseDensity/results.csv: {} stages: + AIMD_ASEMD: + cmd: zntrack run ipsuite.nodes.ASEMD --name AIMD_ASEMD + deps: + - nodes/AIMD/CP2KSinglePoint/atoms.h5 + - nodes/AIMD/CP2KSinglePoint/cp2k + - nodes/AIMD/CP2KSinglePoint/node-meta.json + - nodes/AIMD/ConfigurationSelection/node-meta.json + - nodes/AIMD/ConfigurationSelection/selected_configurations.json + - nodes/AIMD/ConfigurationSelection/selection.png + metrics: + - nodes/AIMD/ASEMD/node-meta.json: + cache: false + - nodes/AIMD/ASEMD/steps_before_stopping.json: + cache: false + outs: + - nodes/AIMD/ASEMD/metrics_dict.csv + - nodes/AIMD/ASEMD/model + - nodes/AIMD/ASEMD/trajectory.h5 + params: + - AIMD_ASEMD + - AIMD_ASEMD+thermostat + AIMD_AnalyseDensity: + cmd: zntrack run ipsuite.nodes.AnalyseDensity --name AIMD_AnalyseDensity + deps: + - nodes/AIMD/ASEMD/metrics_dict.csv + - nodes/AIMD/ASEMD/model + - nodes/AIMD/ASEMD/node-meta.json + - nodes/AIMD/ASEMD/steps_before_stopping.json + - nodes/AIMD/ASEMD/trajectory.h5 + metrics: + - nodes/AIMD/AnalyseDensity/density.json: + cache: false + - nodes/AIMD/AnalyseDensity/node-meta.json: + cache: false + outs: + - nodes/AIMD/AnalyseDensity/density.png + - nodes/AIMD/AnalyseDensity/results.csv + params: + - AIMD_AnalyseDensity + AIMD_CP2KSinglePoint: + cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name AIMD_CP2KSinglePoint + deps: + - GTH_BASIS_SETS + - GTH_POTENTIALS + - dftd3.dat + - nodes/AIMD/ConfigurationSelection/node-meta.json + - nodes/AIMD/ConfigurationSelection/selected_configurations.json + - nodes/AIMD/ConfigurationSelection/selection.png + metrics: + - nodes/AIMD/CP2KSinglePoint/node-meta.json: + cache: false + outs: + - nodes/AIMD/CP2KSinglePoint/atoms.h5 + - nodes/AIMD/CP2KSinglePoint/cp2k + params: + - config/cp2k.yaml: null + AIMD_ConfigurationSelection: + cmd: zntrack run ipsuite.nodes.IndexSelection --name AIMD_ConfigurationSelection + deps: + - nodes/classical/AddData/atoms.h5 + - nodes/classical/AddData/node-meta.json + metrics: + - nodes/AIMD/ConfigurationSelection/node-meta.json: + cache: false + outs: + - nodes/AIMD/ConfigurationSelection/selected_configurations.json + - nodes/AIMD/ConfigurationSelection/selection.png + params: + - AIMD_ConfigurationSelection ML0_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML0_ConfigurationSelection deps: @@ -264,7 +336,7 @@ stages: - nodes/ML0/MLModel/val_atoms.extxyz params: - ML0_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML0_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML0_Prediction deps: @@ -374,7 +446,7 @@ stages: - nodes/ML10/CP2KSinglePoint/atoms.h5 - nodes/ML10/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML10_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML10_ConfigurationSelection deps: @@ -587,7 +659,7 @@ stages: - nodes/ML10/MLModel/val_atoms.extxyz params: - ML10_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML10_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML10_Prediction deps: @@ -647,7 +719,7 @@ stages: - nodes/ML11_MultiPack/CP2KSinglePoint/atoms.h5 - nodes/ML11_MultiPack/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML11_MultiPack_EnergyHistogram: cmd: zntrack run ipsuite.nodes.EnergyHistogram --name ML11_MultiPack_EnergyHistogram deps: @@ -810,7 +882,7 @@ stages: - nodes/ML11_MultiPack/MLModel/val_atoms.extxyz params: - ML11_MultiPack_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML11_MultiPack_MultiPackmol: cmd: zntrack run ipsuite.nodes.MultiPackmol --name ML11_MultiPack_MultiPackmol deps: @@ -968,7 +1040,7 @@ stages: - nodes/ML12/CP2KSinglePoint/atoms.h5 - nodes/ML12/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML12_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML12_ConfigurationSelection deps: @@ -1205,7 +1277,7 @@ stages: - nodes/ML12/MLModel/val_atoms.extxyz params: - ML12_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML12_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML12_Prediction deps: @@ -1291,7 +1363,7 @@ stages: - nodes/ML13/CP2KSinglePoint/atoms.h5 - nodes/ML13/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML13_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML13_ConfigurationSelection deps: @@ -1427,7 +1499,7 @@ stages: - nodes/ML13/MLModel/val_atoms.extxyz params: - ML13_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML13_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML13_Prediction deps: @@ -1514,7 +1586,7 @@ stages: - nodes/ML14/CP2KSinglePoint/atoms.h5 - nodes/ML14/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML14_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML14_ConfigurationSelection deps: @@ -1784,7 +1856,7 @@ stages: - nodes/ML14/MLModel/val_atoms.extxyz params: - ML14_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML14_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML14_Prediction deps: @@ -1892,7 +1964,7 @@ stages: - nodes/ML1/CP2KSinglePoint/atoms.h5 - nodes/ML1/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML1_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML1_ConfigurationSelection deps: @@ -1997,7 +2069,7 @@ stages: - nodes/ML1/MLModel/val_atoms.extxyz params: - ML1_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML1_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML1_Prediction deps: @@ -2106,7 +2178,7 @@ stages: - nodes/ML2/CP2KSinglePoint/atoms.h5 - nodes/ML2/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML2_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML2_ConfigurationSelection deps: @@ -2223,7 +2295,7 @@ stages: - nodes/ML2/MLModel/val_atoms.extxyz params: - ML2_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML2_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML2_Prediction deps: @@ -2332,7 +2404,7 @@ stages: - nodes/ML3/CP2KSinglePoint/atoms.h5 - nodes/ML3/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML3_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML3_ConfigurationSelection deps: @@ -2461,7 +2533,7 @@ stages: - nodes/ML3/MLModel/val_atoms.extxyz params: - ML3_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML3_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML3_Prediction deps: @@ -2570,7 +2642,7 @@ stages: - nodes/ML4/CP2KSinglePoint/atoms.h5 - nodes/ML4/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML4_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML4_ConfigurationSelection deps: @@ -2711,7 +2783,7 @@ stages: - nodes/ML4/MLModel/val_atoms.extxyz params: - ML4_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML4_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML4_Prediction deps: @@ -2821,7 +2893,7 @@ stages: - nodes/ML5/CP2KSinglePoint/atoms.h5 - nodes/ML5/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML5_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML5_ConfigurationSelection deps: @@ -2974,7 +3046,7 @@ stages: - nodes/ML5/MLModel/val_atoms.extxyz params: - ML5_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML5_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML5_Prediction deps: @@ -3084,7 +3156,7 @@ stages: - nodes/ML6/CP2KSinglePoint/atoms.h5 - nodes/ML6/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML6_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML6_ConfigurationSelection deps: @@ -3249,7 +3321,7 @@ stages: - nodes/ML6/MLModel/val_atoms.extxyz params: - ML6_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML6_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML6_Prediction deps: @@ -3359,7 +3431,7 @@ stages: - nodes/ML7/CP2KSinglePoint/atoms.h5 - nodes/ML7/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML7_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML7_ConfigurationSelection deps: @@ -3536,7 +3608,7 @@ stages: - nodes/ML7/MLModel/val_atoms.extxyz params: - ML7_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML7_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML7_Prediction deps: @@ -3646,7 +3718,7 @@ stages: - nodes/ML8/CP2KSinglePoint/atoms.h5 - nodes/ML8/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML8_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML8_ConfigurationSelection deps: @@ -3835,7 +3907,7 @@ stages: - nodes/ML8/MLModel/val_atoms.extxyz params: - ML8_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML8_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML8_Prediction deps: @@ -3945,7 +4017,7 @@ stages: - nodes/ML9/CP2KSinglePoint/atoms.h5 - nodes/ML9/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML9_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML9_ConfigurationSelection deps: @@ -4146,7 +4218,7 @@ stages: - nodes/ML9/MLModel/val_atoms.extxyz params: - ML9_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML9_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML9_Prediction deps: @@ -4431,7 +4503,7 @@ stages: - nodes/VS/CP2KSinglePoint/atoms.h5 - nodes/VS/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null VS_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.RandomSelection --name VS_ConfigurationSelection deps: @@ -4648,7 +4720,7 @@ stages: - nodes/VS/MLModel/val_atoms.extxyz params: - VS_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null VS_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name VS_Prediction deps: @@ -4743,7 +4815,7 @@ stages: - nodes/classical/CP2KSinglePoint/atoms.h5 - nodes/classical/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null classical_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.RandomSelection --name classical_ConfigurationSelection deps: @@ -4854,7 +4926,7 @@ stages: - nodes/classical/MLModel/val_atoms.extxyz params: - classical_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null classical_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name classical_Prediction deps: @@ -4967,7 +5039,7 @@ stages: - nodes/final/MLModel/val_atoms.extxyz params: - final_MLModel - - config/final.yaml: + - config/final.yaml: null final_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name final_Prediction deps: @@ -5079,7 +5151,7 @@ stages: - nodes/final_ensemble/MLModel/val_atoms.extxyz params: - final_ensemble_MLModel - - config/final_ensemble.yaml: + - config/final_ensemble.yaml: null final_ensemble_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name final_ensemble_Prediction deps: @@ -5122,6 +5194,31 @@ stages: - nodes/final_ensemble/PredictionMetrics/stress_deviatoric_df.csv - nodes/final_ensemble/PredictionMetrics/stress_df.csv - nodes/final_ensemble/PredictionMetrics/stress_hydrostatic_df.csv + final_ensemble_PredictionMetrics_1: + cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_ensemble_PredictionMetrics_1 + deps: + - nodes/final_ensemble/Prediction_1/atoms.h5 + - nodes/final_ensemble/Prediction_1/node-meta.json + metrics: + - nodes/final_ensemble/PredictionMetrics_1/deviat_stress.json: + cache: false + - nodes/final_ensemble/PredictionMetrics_1/energy.json: + cache: false + - nodes/final_ensemble/PredictionMetrics_1/forces.json: + cache: false + - nodes/final_ensemble/PredictionMetrics_1/hydro_stress.json: + cache: false + - nodes/final_ensemble/PredictionMetrics_1/node-meta.json: + cache: false + - nodes/final_ensemble/PredictionMetrics_1/stress.json: + cache: false + outs: + - nodes/final_ensemble/PredictionMetrics_1/energy_df.csv + - nodes/final_ensemble/PredictionMetrics_1/forces_df.csv + - nodes/final_ensemble/PredictionMetrics_1/plots + - nodes/final_ensemble/PredictionMetrics_1/stress_deviatoric_df.csv + - nodes/final_ensemble/PredictionMetrics_1/stress_df.csv + - nodes/final_ensemble/PredictionMetrics_1/stress_hydrostatic_df.csv final_ensemble_Prediction_1: cmd: zntrack run ipsuite.nodes.Prediction --name final_ensemble_Prediction_1 deps: @@ -5182,33 +5279,8 @@ stages: - nodes/final_ensemble/MLModel/node-meta.json - nodes/final_ensemble/MLModel/train_atoms.extxyz - nodes/final_ensemble/MLModel/val_atoms.extxyz - outs: - - nodes/final_ensemble/Prediction_1/atoms.h5 metrics: - nodes/final_ensemble/Prediction_1/node-meta.json: cache: false - final_ensemble_PredictionMetrics_1: - cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_ensemble_PredictionMetrics_1 - deps: - - nodes/final_ensemble/Prediction_1/atoms.h5 - - nodes/final_ensemble/Prediction_1/node-meta.json outs: - - nodes/final_ensemble/PredictionMetrics_1/energy_df.csv - - nodes/final_ensemble/PredictionMetrics_1/forces_df.csv - - nodes/final_ensemble/PredictionMetrics_1/plots - - nodes/final_ensemble/PredictionMetrics_1/stress_deviatoric_df.csv - - nodes/final_ensemble/PredictionMetrics_1/stress_df.csv - - nodes/final_ensemble/PredictionMetrics_1/stress_hydrostatic_df.csv - metrics: - - nodes/final_ensemble/PredictionMetrics_1/deviat_stress.json: - cache: false - - nodes/final_ensemble/PredictionMetrics_1/energy.json: - cache: false - - nodes/final_ensemble/PredictionMetrics_1/forces.json: - cache: false - - nodes/final_ensemble/PredictionMetrics_1/hydro_stress.json: - cache: false - - nodes/final_ensemble/PredictionMetrics_1/node-meta.json: - cache: false - - nodes/final_ensemble/PredictionMetrics_1/stress.json: - cache: false + - nodes/final_ensemble/Prediction_1/atoms.h5 diff --git a/main.py b/main.py index 7b807be..c4a102f 100644 --- a/main.py +++ b/main.py @@ -55,6 +55,40 @@ sampling_rate=10, ) +thermostat = ips.calculators.NPTThermostat( + time_step=0.5, + temperature=303, + pressure=1.01325 * units.bar, + ttime=25 * units.fs, + pfactor=(75 * units.fs) ** 2, + tetragonal_strain=True, + ) + +with project.group("AIMD") as aimd_grp: + start_conf = ips.configuration_selection.IndexSelection( + data.atoms, + indices=[2000,] + ) + + aimd_model = ips.calculators.CP2KSinglePoint( + data=start_conf.atoms, + cp2k_params="config/cp2k.yaml", + cp2k_files=["GTH_BASIS_SETS", "GTH_POTENTIALS", "dftd3.dat"], + ) + + aimd = ips.calculators.ASEMD( + data=start_conf.atoms, + data_id=-1, + model=aimd_model, + thermostat=thermostat, + steps=13_200, + sampling_rate=1, + dump_rate=100, + ) + + density = ips.analysis.AnalyseDensity(data=aimd.atoms) + + with project.group("ML0"): kernel_selection = ips.models.apax.BatchKernelSelection( data=train_data.excluded_atoms, @@ -536,4 +570,4 @@ prediction = ips.analysis.Prediction(data=train_data, model=model) metrics = ips.analysis.PredictionMetrics(data=prediction) -project.build(nodes=[final]) +project.build(nodes=[aimd_grp]) diff --git a/nodes/AIMD/ASEMD/.gitignore b/nodes/AIMD/ASEMD/.gitignore new file mode 100644 index 0000000..c8ee395 --- /dev/null +++ b/nodes/AIMD/ASEMD/.gitignore @@ -0,0 +1,3 @@ +/trajectory.h5 +/model +/metrics_dict.csv diff --git a/nodes/AIMD/ASEMD/node-meta.json b/nodes/AIMD/ASEMD/node-meta.json new file mode 100644 index 0000000..74a6963 --- /dev/null +++ b/nodes/AIMD/ASEMD/node-meta.json @@ -0,0 +1 @@ +{"uuid": "cd255ff2-aa42-4e16-a6cd-f1a9237ca196"} \ No newline at end of file diff --git a/nodes/AIMD/ASEMD/steps_before_stopping.json b/nodes/AIMD/ASEMD/steps_before_stopping.json new file mode 100644 index 0000000..d7d17fc --- /dev/null +++ b/nodes/AIMD/ASEMD/steps_before_stopping.json @@ -0,0 +1 @@ +-1 \ No newline at end of file diff --git a/nodes/AIMD/AnalyseDensity/.gitignore b/nodes/AIMD/AnalyseDensity/.gitignore new file mode 100644 index 0000000..b1d7173 --- /dev/null +++ b/nodes/AIMD/AnalyseDensity/.gitignore @@ -0,0 +1,2 @@ +/results.csv +/density.png diff --git a/nodes/AIMD/AnalyseDensity/density.json b/nodes/AIMD/AnalyseDensity/density.json new file mode 100644 index 0000000..2628010 --- /dev/null +++ b/nodes/AIMD/AnalyseDensity/density.json @@ -0,0 +1,4 @@ +{ + "density": 1107.791955911932, + "std": 28.05726060677191 +} \ No newline at end of file diff --git a/nodes/AIMD/AnalyseDensity/node-meta.json b/nodes/AIMD/AnalyseDensity/node-meta.json new file mode 100644 index 0000000..f7a264a --- /dev/null +++ b/nodes/AIMD/AnalyseDensity/node-meta.json @@ -0,0 +1 @@ +{"uuid": "96360e64-0642-4054-907c-91b59b2655dd"} \ No newline at end of file diff --git a/nodes/AIMD/CP2KSinglePoint/.gitignore b/nodes/AIMD/CP2KSinglePoint/.gitignore new file mode 100644 index 0000000..d0f4574 --- /dev/null +++ b/nodes/AIMD/CP2KSinglePoint/.gitignore @@ -0,0 +1,2 @@ +/cp2k +/atoms.h5 diff --git a/nodes/AIMD/CP2KSinglePoint/node-meta.json b/nodes/AIMD/CP2KSinglePoint/node-meta.json new file mode 100644 index 0000000..094501c --- /dev/null +++ b/nodes/AIMD/CP2KSinglePoint/node-meta.json @@ -0,0 +1 @@ +{"uuid": "e0f6d873-64a4-4978-9c86-140653846ce9"} \ No newline at end of file diff --git a/nodes/AIMD/ConfigurationSelection/.gitignore b/nodes/AIMD/ConfigurationSelection/.gitignore new file mode 100644 index 0000000..83e390d --- /dev/null +++ b/nodes/AIMD/ConfigurationSelection/.gitignore @@ -0,0 +1,2 @@ +/selected_configurations.json +/selection.png diff --git a/nodes/AIMD/ConfigurationSelection/node-meta.json b/nodes/AIMD/ConfigurationSelection/node-meta.json new file mode 100644 index 0000000..fb514ec --- /dev/null +++ b/nodes/AIMD/ConfigurationSelection/node-meta.json @@ -0,0 +1 @@ +{"uuid": "df38abb8-600a-4b2e-98e2-ce1836470ba6"} \ No newline at end of file diff --git a/params.yaml b/params.yaml index e5d108b..a00471a 100644 --- a/params.yaml +++ b/params.yaml @@ -1,3 +1,30 @@ +AIMD_ASEMD: + data_id: -1 + dump_rate: 100 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 1 + seed: 42 + steps: 13200 + use_momenta: false + wrap: false +AIMD_ASEMD+thermostat: + pfactor: 54.27299976036698 + pressure: 6.324209121801212e-07 + temperature: 303 + tetragonal_strain: true + time_step: 0.5 + ttime: 2.455673697116016 +AIMD_AnalyseDensity: + end: null + start: 0 + window: 1000 +AIMD_ConfigurationSelection: + indices: + - 2000 ML0_ConfigurationSelection: base_feature_map: layer_name: dense_2 diff --git a/submit_cpu.sh b/submit_cpu.sh index 80a1dd3..3d6dcb2 100644 --- a/submit_cpu.sh +++ b/submit_cpu.sh @@ -3,7 +3,7 @@ #SBATCH --ntasks=32 #SBATCH --cpus-per-task=8 #SBATCH --time=48:00:00 -#SBATCH --mem=32gb +#SBATCH --mem=64gb source ~/.bashrc diff --git a/zntrack.json b/zntrack.json index c7e056c..f5a91b1 100644 --- a/zntrack.json +++ b/zntrack.json @@ -16237,5 +16237,173 @@ "_type": "pathlib.Path", "value": "nodes/final_ensemble/PredictionMetrics_1" } + }, + "AIMD_ConfigurationSelection": { + "data": { + "classical_AddData": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "AddData", + "name": "classical_AddData", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + } + }, + "data_file": null, + "exclude": null, + "exclude_configurations": null, + "img_selection": { + "_type": "pathlib.Path", + "value": "$nwd$/selection.png" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/AIMD/ConfigurationSelection" + } + }, + "AIMD_CP2KSinglePoint": { + "cp2k_directory": { + "_type": "pathlib.Path", + "value": "$nwd$/cp2k" + }, + "cp2k_files": [ + "GTH_BASIS_SETS", + "GTH_POTENTIALS", + "dftd3.dat" + ], + "cp2k_params": "config/cp2k.yaml", + "cp2k_shell": null, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "IndexSelection", + "name": "AIMD_ConfigurationSelection", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "data_file": null, + "output_file": { + "_type": "pathlib.Path", + "value": "$nwd$/atoms.h5" + }, + "wfn_restart_file": null, + "wfn_restart_node": null, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/AIMD/CP2KSinglePoint" + } + }, + "AIMD_ASEMD": { + "checker_list": null, + "constraint_list": null, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "IndexSelection", + "name": "AIMD_ConfigurationSelection", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "data_file": null, + "model": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "CP2KSinglePoint", + "name": "AIMD_CP2KSinglePoint", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "model_outs": { + "_type": "pathlib.Path", + "value": "$nwd$/model" + }, + "modifier": null, + "thermostat": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "NPTThermostat", + "name": "AIMD_ASEMD+thermostat", + "remote": null, + "rev": null + } + }, + "traj_file": { + "_type": "pathlib.Path", + "value": "$nwd$/trajectory.h5" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/AIMD/ASEMD" + } + }, + "AIMD_ASEMD+thermostat": { + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/AIMD_ASEMD+thermostat" + } + }, + "AIMD_AnalyseDensity": { + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "ASEMD", + "name": "AIMD_ASEMD", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "figure": { + "_type": "pathlib.Path", + "value": "$nwd$/density.png" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/AIMD/AnalyseDensity" + } } } \ No newline at end of file