diff --git a/config/md.yaml b/config/md.yaml new file mode 100644 index 0000000..345a495 --- /dev/null +++ b/config/md.yaml @@ -0,0 +1,11 @@ +ensemble: + name: nvt + dt: 0.5 # fs time step + temperature: 293 # K + +duration: 20_000_000 # fs +n_inner: 5000 # compiled inner steps +sampling_rate: 200 # dump interval +buffer_size: 1000 +dr_threshold: 0.5 # Neighborlist skin +checkpoint_interval: 200 diff --git a/config/ml17.yaml b/config/ml17.yaml new file mode 100644 index 0000000..877dc10 --- /dev/null +++ b/config/ml17.yaml @@ -0,0 +1,57 @@ +n_epochs: 2000 +seed: 1 +n_models: 1 +n_jitted_steps: 8 +patience: 250 + +data: + batch_size: 1 + scale_method: per_element_force_rms_scale + shift_method: per_element_regression_shift + shift_options: + energy_regularisation: 1.0 + valid_batch_size: 70 +loss: +- name: energy +- name: forces + weight: 4.0 +- name: stress + weight: 0.2 + +metrics: +- name: energy + reductions: + - mae +- name: forces + reductions: + - mae +- name: stress + reductions: + - mae + +model: + n_basis: 7 + n_radial: 5 + nn: + - 512 + - 512 + r_max: 6.0 + r_min: 0.7 + + b_init: zeros + emb_init: uniform + + calc_stress: true + use_zbl: false + + descriptor_dtype: fp32 + readout_dtype: fp32 + scale_shift_dtype: fp32 + +optimizer: + opt_name: adam + emb_lr: 0.01 + nn_lr: 0.005 + scale_lr: 0.001 + shift_lr: 0.05 + zbl_lr: 0.001 diff --git a/dvc.lock b/dvc.lock index 1f011a0..bbeb7ed 100644 --- a/dvc.lock +++ b/dvc.lock @@ -27147,3 +27147,719 @@ stages: md5: 97a745d67e4b8098190e50cb8a906cda.dir size: 33603 nfiles: 1 + depl_SmilesToAtoms: + cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name depl_SmilesToAtoms + params: + params.yaml: + depl_SmilesToAtoms: + cell: + optimizer: UFF + seed: 1234 + smiles: '[B-](F)(F)(F)F' + outs: + - path: nodes/depl/SmilesToAtoms/atoms.h5 + hash: md5 + md5: 181a42114d5c08d6ac24e8ce30a8f82b + size: 27968 + - path: nodes/depl/SmilesToAtoms/molecule.png + hash: md5 + md5: f4d4f99183d79b889d60ffaf0d08a5a7 + size: 2975 + - path: nodes/depl/SmilesToAtoms/node-meta.json + hash: md5 + md5: 5a244a5c7469a433de92fdfe4ceee2dd + size: 48 + depl_SmilesToAtoms_1: + cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name depl_SmilesToAtoms_1 + params: + params.yaml: + depl_SmilesToAtoms_1: + cell: + optimizer: UFF + seed: 1234 + smiles: CCCCN1C=C[N+](=C1)C + outs: + - path: nodes/depl/SmilesToAtoms_1/atoms.h5 + hash: md5 + md5: 744f94e60270ed284980820ff3038f19 + size: 27968 + - path: nodes/depl/SmilesToAtoms_1/molecule.png + hash: md5 + md5: a9e6627ebd24d022ae34219e921b7e5f + size: 7818 + - path: nodes/depl/SmilesToAtoms_1/node-meta.json + hash: md5 + md5: 91396f35ba991cd25ae6f5169a5c9d71 + size: 48 + depl_Packmol: + cmd: zntrack run ipsuite.nodes.Packmol --name depl_Packmol + deps: + - path: nodes/depl/SmilesToAtoms/atoms.h5 + hash: md5 + md5: 181a42114d5c08d6ac24e8ce30a8f82b + size: 27968 + - path: nodes/depl/SmilesToAtoms/molecule.png + hash: md5 + md5: f4d4f99183d79b889d60ffaf0d08a5a7 + size: 2975 + - path: nodes/depl/SmilesToAtoms/node-meta.json + hash: md5 + md5: 5a244a5c7469a433de92fdfe4ceee2dd + size: 48 + - path: nodes/depl/SmilesToAtoms_1/atoms.h5 + hash: md5 + md5: 744f94e60270ed284980820ff3038f19 + size: 27968 + - path: nodes/depl/SmilesToAtoms_1/molecule.png + hash: md5 + md5: a9e6627ebd24d022ae34219e921b7e5f + size: 7818 + - path: nodes/depl/SmilesToAtoms_1/node-meta.json + hash: md5 + md5: 91396f35ba991cd25ae6f5169a5c9d71 + size: 48 + params: + params.yaml: + depl_Packmol: + box: + count: + - 1 + - 1 + data_ids: + density: 1210 + pbc: false + tolerance: 2.0 + outs: + - path: nodes/depl/Packmol/atoms.h5 + hash: md5 + md5: 2400ddfca5ec50ebe880626f190e0797 + size: 27968 + - path: nodes/depl/Packmol/node-meta.json + hash: md5 + md5: 183c2b460f416178653dc0ea9b0a9fdd + size: 48 + - path: nodes/depl/Packmol/packmol + hash: md5 + md5: 9211f580932fa95a1d122b0e2be6699c.dir + size: 3841 + nfiles: 4 + depl_Packmol_1: + cmd: zntrack run ipsuite.nodes.Packmol --name depl_Packmol_1 + deps: + - path: nodes/depl/Packmol/atoms.h5 + hash: md5 + md5: 2400ddfca5ec50ebe880626f190e0797 + size: 27968 + - path: nodes/depl/Packmol/node-meta.json + hash: md5 + md5: 183c2b460f416178653dc0ea9b0a9fdd + size: 48 + - path: nodes/depl/Packmol/packmol + hash: md5 + md5: 9211f580932fa95a1d122b0e2be6699c.dir + size: 3841 + nfiles: 4 + params: + params.yaml: + depl_Packmol_1: + box: + count: + - 16 + data_ids: + density: 900 + pbc: true + tolerance: 2.0 + outs: + - path: nodes/depl/Packmol_1/atoms.h5 + hash: md5 + md5: 7ec77fd6549c61434a9b28b7715027a8 + size: 43328 + - path: nodes/depl/Packmol_1/node-meta.json + hash: md5 + md5: 4dab86e07acb5e1b620a83587ef489a4 + size: 48 + - path: nodes/depl/Packmol_1/packmol + hash: md5 + md5: ac2a1f78e24d4acec487ee8d320e3c86.dir + size: 28854 + nfiles: 3 + depl_ASEGeoOpt: + cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt + deps: + - path: nodes/ML17_training/MLModel_1/apax_model + hash: md5 + md5: d7678afd0cb163733fbfd407fef3eae2.dir + size: 85054069 + nfiles: 10 + - path: nodes/ML17_training/MLModel_1/log.csv + hash: md5 + md5: 3607ffe4448f09d2af3c742921523997 + size: 127837 + - path: nodes/ML17_training/MLModel_1/metrics.json + hash: md5 + md5: 5c46e3b2a689b5baa294c3d5b98daad0 + size: 390 + - path: nodes/ML17_training/MLModel_1/node-meta.json + hash: md5 + md5: a8064a6ba7ef8aa7568f1da78634ae81 + size: 48 + - path: nodes/ML17_training/MLModel_1/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_1/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + - path: nodes/depl/Packmol_1/atoms.h5 + hash: md5 + md5: 7ec77fd6549c61434a9b28b7715027a8 + size: 43328 + - path: nodes/depl/Packmol_1/node-meta.json + hash: md5 + md5: 4dab86e07acb5e1b620a83587ef489a4 + size: 48 + - path: nodes/depl/Packmol_1/packmol + hash: md5 + md5: ac2a1f78e24d4acec487ee8d320e3c86.dir + size: 28854 + nfiles: 3 + params: + params.yaml: + depl_ASEGeoOpt: + data_id: -1 + dump_rate: 1000 + init_kwargs: {} + optimizer: FIRE + repeat: + - 1 + - 1 + - 1 + run_kwargs: + fmax: 0.05 + outs: + - path: nodes/depl/ASEGeoOpt/model_outs + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEGeoOpt/node-meta.json + hash: md5 + md5: fe39d4aaaae596691bf44639f50031f0 + size: 48 + - path: nodes/depl/ASEGeoOpt/trajectory.h5 + hash: md5 + md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4 + size: 6554344 + depl_ASEMD: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD + deps: + - path: nodes/ML17_training/MLModel_1/apax_model + hash: md5 + md5: d7678afd0cb163733fbfd407fef3eae2.dir + size: 85054069 + nfiles: 10 + - path: nodes/ML17_training/MLModel_1/log.csv + hash: md5 + md5: 3607ffe4448f09d2af3c742921523997 + size: 127837 + - path: nodes/ML17_training/MLModel_1/metrics.json + hash: md5 + md5: 5c46e3b2a689b5baa294c3d5b98daad0 + size: 390 + - path: nodes/ML17_training/MLModel_1/node-meta.json + hash: md5 + md5: a8064a6ba7ef8aa7568f1da78634ae81 + size: 48 + - path: nodes/ML17_training/MLModel_1/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_1/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + - path: nodes/depl/ASEGeoOpt/model_outs + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEGeoOpt/node-meta.json + hash: md5 + md5: fe39d4aaaae596691bf44639f50031f0 + size: 48 + - path: nodes/depl/ASEGeoOpt/trajectory.h5 + hash: md5 + md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4 + size: 6554344 + params: + params.yaml: + depl_ASEMD: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 10000 + use_momenta: false + wrap: false + depl_ASEMD+modifier+0: + cell: + density: 1204 + depl_ASEMD+thermostat: + friction: 0.01 + temperature: 293 + time_step: 0.5 + outs: + - path: nodes/depl/ASEMD/metrics_dict.csv + hash: md5 + md5: f9992334b6865f16209f99bdbba68f53 + size: 42098 + - path: nodes/depl/ASEMD/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD/node-meta.json + hash: md5 + md5: cf2e267d8703152694ec822e5024d479 + size: 64 + - path: nodes/depl/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD/trajectory.h5 + hash: md5 + md5: 690f620a32436711fdbee04f66286a61 + size: 50790792 + depl_ASEMD_1: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1 + deps: + - path: nodes/ML17_training/MLModel_1/apax_model + hash: md5 + md5: d7678afd0cb163733fbfd407fef3eae2.dir + size: 85054069 + nfiles: 10 + - path: nodes/ML17_training/MLModel_1/log.csv + hash: md5 + md5: 3607ffe4448f09d2af3c742921523997 + size: 127837 + - path: nodes/ML17_training/MLModel_1/metrics.json + hash: md5 + md5: 5c46e3b2a689b5baa294c3d5b98daad0 + size: 390 + - path: nodes/ML17_training/MLModel_1/node-meta.json + hash: md5 + md5: a8064a6ba7ef8aa7568f1da78634ae81 + size: 48 + - path: nodes/ML17_training/MLModel_1/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_1/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + - path: nodes/depl/ASEMD/metrics_dict.csv + hash: md5 + md5: f9992334b6865f16209f99bdbba68f53 + size: 42098 + - path: nodes/depl/ASEMD/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD/node-meta.json + hash: md5 + md5: cf2e267d8703152694ec822e5024d479 + size: 64 + - path: nodes/depl/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD/trajectory.h5 + hash: md5 + md5: 690f620a32436711fdbee04f66286a61 + size: 50790792 + params: + params.yaml: + depl_ASEMD_1: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 10000 + use_momenta: true + wrap: false + depl_ASEMD_1+thermostat: + friction: 0.01 + temperature: 293 + time_step: 0.5 + outs: + - path: nodes/depl/ASEMD_1/metrics_dict.csv + hash: md5 + md5: 070e36f16a3f963b3efa4452bf6a8c9a + size: 41987 + - path: nodes/depl/ASEMD_1/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD_1/node-meta.json + hash: md5 + md5: 23c29f3c178061396f58c035aa14e466 + size: 64 + - path: nodes/depl/ASEMD_1/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD_1/trajectory.h5 + hash: md5 + md5: 0dc924b787779e5f2ceed102dbff1cb1 + size: 50790792 + ML17_training_MLModel_4: + cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_4 + deps: + - path: nodes/ML17_datasets/TorchD3/atoms.h5 + hash: md5 + md5: 6103d479069f56ac746959755e327a0b + size: 27607783 + - path: nodes/ML17_datasets/TorchD3/node-meta.json + hash: md5 + md5: d0e6461f7f24fe4d41cbacbb302cef27 + size: 48 + - path: nodes/ML17_datasets/TorchD3_1/atoms.h5 + hash: md5 + md5: 0a1b6f6259665c84c1a8650550681465 + size: 4800256 + - path: nodes/ML17_datasets/TorchD3_1/node-meta.json + hash: md5 + md5: 0d372a7cd0f4b3fa4b0e96211ae3d6ed + size: 48 + params: + params.yaml: + ML17_training_MLModel_4: + jax_enable_x64: true + use_energy: true + use_forces: true + use_stresses: false + config/ml17.yaml: + data: + batch_size: 1 + scale_method: per_element_force_rms_scale + shift_method: per_element_regression_shift + shift_options: + energy_regularisation: 1.0 + valid_batch_size: 70 + loss: + - name: energy + - name: forces + weight: 4.0 + - name: stress + weight: 0.2 + metrics: + - name: energy + reductions: + - mae + - name: forces + reductions: + - mae + - name: stress + reductions: + - mae + model: + n_basis: 7 + n_radial: 5 + nn: + - 512 + - 512 + r_max: 6.0 + r_min: 0.7 + b_init: zeros + emb_init: uniform + calc_stress: true + use_zbl: false + descriptor_dtype: fp32 + readout_dtype: fp32 + scale_shift_dtype: fp32 + n_epochs: 2000 + n_jitted_steps: 8 + n_models: 1 + optimizer: + opt_name: adam + emb_lr: 0.01 + nn_lr: 0.005 + scale_lr: 0.001 + shift_lr: 0.05 + zbl_lr: 0.001 + patience: 250 + seed: 1 + outs: + - path: nodes/ML17_training/MLModel_4/apax_model + hash: md5 + md5: aa63efa602888b8f74e91f671432b379.dir + size: 42819635 + nfiles: 10 + - path: nodes/ML17_training/MLModel_4/log.csv + hash: md5 + md5: 53b7282023a40208b91c5bf2ecfae07a + size: 76158 + - path: nodes/ML17_training/MLModel_4/metrics.json + hash: md5 + md5: 7448ea4e0b38638fb7745b44022ad406 + size: 386 + - path: nodes/ML17_training/MLModel_4/node-meta.json + hash: md5 + md5: 43eef97813ef3779e67c40c0f41b86ee + size: 48 + - path: nodes/ML17_training/MLModel_4/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_4/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + ML17_eval_Prediction_4: + cmd: zntrack run ipsuite.nodes.Prediction --name ML17_eval_Prediction_4 + deps: + - path: nodes/ML17_datasets/TorchD3_3/atoms.h5 + hash: md5 + md5: 184e2c8088e5742613133f5d3c26ddd3 + size: 4800256 + - path: nodes/ML17_datasets/TorchD3_3/node-meta.json + hash: md5 + md5: 7b1e5f500c89090f471bffb586e96145 + size: 48 + - path: nodes/ML17_training/MLModel_4/apax_model + hash: md5 + md5: aa63efa602888b8f74e91f671432b379.dir + size: 42819635 + nfiles: 10 + - path: nodes/ML17_training/MLModel_4/log.csv + hash: md5 + md5: 53b7282023a40208b91c5bf2ecfae07a + size: 76158 + - path: nodes/ML17_training/MLModel_4/metrics.json + hash: md5 + md5: 7448ea4e0b38638fb7745b44022ad406 + size: 386 + - path: nodes/ML17_training/MLModel_4/node-meta.json + hash: md5 + md5: 43eef97813ef3779e67c40c0f41b86ee + size: 48 + - path: nodes/ML17_training/MLModel_4/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_4/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + outs: + - path: nodes/ML17_eval/Prediction_4/atoms.h5 + hash: md5 + md5: 81d8f94e120865b286ff9da095a9b6c3 + size: 4794072 + - path: nodes/ML17_eval/Prediction_4/node-meta.json + hash: md5 + md5: 99eb48b1b224886b20326c953ac8756d + size: 48 + ML17_eval_PredictionMetrics_4: + cmd: zntrack run ipsuite.nodes.PredictionMetrics --name ML17_eval_PredictionMetrics_4 + deps: + - path: nodes/ML17_eval/Prediction_4/atoms.h5 + hash: md5 + md5: 81d8f94e120865b286ff9da095a9b6c3 + size: 4794072 + - path: nodes/ML17_eval/Prediction_4/node-meta.json + hash: md5 + md5: 99eb48b1b224886b20326c953ac8756d + size: 48 + outs: + - path: nodes/ML17_eval/PredictionMetrics_4/deviat_stress.json + hash: md5 + md5: 93f55816c2a173f1b72c5495888ce105 + size: 205 + - path: nodes/ML17_eval/PredictionMetrics_4/energy.json + hash: md5 + md5: a5a32c26024dab592fe7deea8d15e3d2 + size: 188 + - path: nodes/ML17_eval/PredictionMetrics_4/energy_df.csv + hash: md5 + md5: b74652e6da0d0a093170bb606cf1c338 + size: 12044 + - path: nodes/ML17_eval/PredictionMetrics_4/forces.json + hash: md5 + md5: a195ec6bdab0ccbf511f60d373dea1de + size: 187 + - path: nodes/ML17_eval/PredictionMetrics_4/forces_df.csv + hash: md5 + md5: 56e51565c7e19d77be3d2f81fcfa1c9b + size: 13088341 + - path: nodes/ML17_eval/PredictionMetrics_4/hydro_stress.json + hash: md5 + md5: d0b21f2ceedc51973bff79257709e80a + size: 208 + - path: nodes/ML17_eval/PredictionMetrics_4/node-meta.json + hash: md5 + md5: a828166fe63a60f1ab52a761ae298b36 + size: 48 + - path: nodes/ML17_eval/PredictionMetrics_4/plots + hash: md5 + md5: e18104f4f26a0a04d0a360b4543ab336.dir + size: 331741 + nfiles: 5 + - path: nodes/ML17_eval/PredictionMetrics_4/stress.json + hash: md5 + md5: 6f7774beb3c092fb72fdf2c6d41f38b3 + size: 207 + - path: nodes/ML17_eval/PredictionMetrics_4/stress_deviatoric_df.csv + hash: md5 + md5: b516382a923ea9652633fe9c28068e11 + size: 123780 + - path: nodes/ML17_eval/PredictionMetrics_4/stress_df.csv + hash: md5 + md5: 7e7cf887d59fcb0d3f5db178d1391c64 + size: 122811 + - path: nodes/ML17_eval/PredictionMetrics_4/stress_hydrostatic_df.csv + hash: md5 + md5: f6f3ac2982db046cd38928a3a5dbd3e1 + size: 13181 + ML17_eval_ForceDecomposition_4: + cmd: zntrack run ipsuite.nodes.ForceDecomposition --name ML17_eval_ForceDecomposition_4 + deps: + - path: nodes/ML17_eval/Prediction_4/atoms.h5 + hash: md5 + md5: 81d8f94e120865b286ff9da095a9b6c3 + size: 4794072 + - path: nodes/ML17_eval/Prediction_4/node-meta.json + hash: md5 + md5: 99eb48b1b224886b20326c953ac8756d + size: 48 + outs: + - path: nodes/ML17_eval/ForceDecomposition_4/histogram.png + hash: md5 + md5: 5863c19f3b6442d3142afea697c063ba + size: 121300 + - path: nodes/ML17_eval/ForceDecomposition_4/node-meta.json + hash: md5 + md5: 6719dbb2703026fd790b9b14c0bff9de + size: 48 + - path: nodes/ML17_eval/ForceDecomposition_4/rot_force.png + hash: md5 + md5: 7486a7c0fc61722790bd96b43908cb7a + size: 121686 + - path: nodes/ML17_eval/ForceDecomposition_4/rot_forces.json + hash: md5 + md5: 86954fd139025a6078b95e5a6b96130c + size: 191 + - path: nodes/ML17_eval/ForceDecomposition_4/trans_force.png + hash: md5 + md5: 5783ee437bac9833662c7c7184b451c3 + size: 114268 + - path: nodes/ML17_eval/ForceDecomposition_4/trans_forces.json + hash: md5 + md5: 28ff510b76fcccd069494abe44a5315d + size: 191 + - path: nodes/ML17_eval/ForceDecomposition_4/vib_force.png + hash: md5 + md5: 19e79c777453edc769a22a41b33d9a8a + size: 59855 + - path: nodes/ML17_eval/ForceDecomposition_4/vib_forces.json + hash: md5 + md5: c72305565258ac0d3ea75682e7d9112b + size: 190 + - path: nodes/ML17_eval/ForceDecomposition_4/wasserstein_distance.json + hash: md5 + md5: c1eb79de53c976c96c75792660d41afa + size: 551 + depl_ApaxJaxMD: + cmd: zntrack run ipsuite.nodes.ApaxJaxMD --name depl_ApaxJaxMD + deps: + - path: nodes/ML17_training/MLModel_1/apax_model + hash: md5 + md5: d7678afd0cb163733fbfd407fef3eae2.dir + size: 85054069 + nfiles: 10 + - path: nodes/ML17_training/MLModel_1/log.csv + hash: md5 + md5: 3607ffe4448f09d2af3c742921523997 + size: 127837 + - path: nodes/ML17_training/MLModel_1/metrics.json + hash: md5 + md5: 5c46e3b2a689b5baa294c3d5b98daad0 + size: 390 + - path: nodes/ML17_training/MLModel_1/node-meta.json + hash: md5 + md5: a8064a6ba7ef8aa7568f1da78634ae81 + size: 48 + - path: nodes/ML17_training/MLModel_1/train_atoms.extxyz + hash: md5 + md5: 4b24dcda97a81a2018dd430b350725cc + size: 50703910 + - path: nodes/ML17_training/MLModel_1/val_atoms.extxyz + hash: md5 + md5: f610bf1397ca89bf56a9edc2ed047b3d + size: 8933596 + - path: nodes/depl/ASEMD_1/metrics_dict.csv + hash: md5 + md5: d205750be5ae46c161407aebe9acd95f + size: 41997 + - path: nodes/depl/ASEMD_1/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD_1/node-meta.json + hash: md5 + md5: e078a456bc04af626027522a906aa7bd + size: 64 + - path: nodes/depl/ASEMD_1/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD_1/trajectory.h5 + hash: md5 + md5: 6af08c94d13be72cd0c15478087ff4cb + size: 50790792 + params: + params.yaml: + depl_ApaxJaxMD: + data_id: -1 + md_parameter: + repeat: + config/md.yaml: + buffer_size: 1000 + checkpoint_interval: 200 + dr_threshold: 0.5 + duration: 20000000 + ensemble: + name: nvt + dt: 0.5 + temperature: 333 + n_inner: 5000 + sampling_rate: 200 + outs: + - path: nodes/depl/ApaxJaxMD/initial_structure.extxyz + hash: md5 + md5: 8b1cf3ce64664a86afac689c3fec0ac6 + size: 50544 + - path: nodes/depl/ApaxJaxMD/md + hash: md5 + md5: 9978465ba172e09f104267144a6d1b4b.dir + size: 8168584398 + nfiles: 6 + - path: nodes/depl/ApaxJaxMD/node-meta.json + hash: md5 + md5: ca4a4f3af6307c39a449e786ae2bbe2e + size: 64 diff --git a/dvc.yaml b/dvc.yaml index 183a708..d3aee8d 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -259,6 +259,14 @@ plots: - nodes/ML17_eval/EnergyHistogram_2/labels_df.csv: {} - nodes/ML17_eval/EnergyHistogram/labels_df.csv: {} - nodes/ML17_eval/ForcesHistogram_2/labels_df.csv: {} +- nodes/depl/ASEMD/metrics_dict.csv: {} +- nodes/depl/ASEMD_1/metrics_dict.csv: {} +- nodes/ML17_training/MLModel_4/log.csv: + template: dvc_plots/templates/y_log.json + x: epoch + x_label: epochs + y: val_loss + y_label: validation loss stages: ML0_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML0_ConfigurationSelection @@ -344,7 +352,7 @@ 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: @@ -454,7 +462,7 @@ 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: @@ -667,7 +675,7 @@ 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: @@ -727,7 +735,7 @@ 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: @@ -890,7 +898,7 @@ 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: @@ -1048,7 +1056,7 @@ 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: @@ -1285,7 +1293,7 @@ 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: @@ -1371,7 +1379,7 @@ 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: @@ -1507,7 +1515,7 @@ 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: @@ -1594,7 +1602,7 @@ 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: @@ -1864,7 +1872,7 @@ 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: @@ -1952,7 +1960,7 @@ stages: - nodes/ML15/CP2KSinglePoint/atoms.h5 - nodes/ML15/CP2KSinglePoint/cp2k params: - - config/cp2k.yaml: + - config/cp2k.yaml: null ML15_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML15_ConfigurationSelection deps: @@ -2232,7 +2240,7 @@ stages: - nodes/ML15/MLModel/val_atoms.extxyz params: - ML15_MLModel - - config/initial_model.yaml: + - config/initial_model.yaml: null ML15_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML15_Prediction deps: @@ -2339,7 +2347,7 @@ stages: - nodes/ML16/CP2KSinglePoint/atoms.h5 - nodes/ML16/CP2KSinglePoint/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null ML16_CP2KSinglePoint_1: cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name ML16_CP2KSinglePoint_1 deps: @@ -2355,7 +2363,7 @@ stages: - nodes/ML16/CP2KSinglePoint_1/atoms.h5 - nodes/ML16/CP2KSinglePoint_1/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null ML16_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML16_ConfigurationSelection deps: @@ -2495,7 +2503,7 @@ stages: - nodes/ML16/MLModel/val_atoms.extxyz params: - ML16_MLModel - - config/wod3.yaml: + - config/wod3.yaml: null ML16_Prediction: cmd: zntrack run ipsuite.nodes.Prediction --name ML16_Prediction deps: @@ -2562,7 +2570,7 @@ stages: - nodes/ML17_datasets/CP2KSinglePoint/atoms.h5 - nodes/ML17_datasets/CP2KSinglePoint/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null ML17_datasets_CP2KSinglePoint_1: cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name ML17_datasets_CP2KSinglePoint_1 deps: @@ -2581,7 +2589,7 @@ stages: - nodes/ML17_datasets/CP2KSinglePoint_1/atoms.h5 - nodes/ML17_datasets/CP2KSinglePoint_1/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null ML17_datasets_TorchD3: cmd: zntrack run ipsuite.nodes.TorchD3 --name ML17_datasets_TorchD3 deps: @@ -2794,6 +2802,27 @@ stages: - nodes/ML17_eval/ForceDecomposition_3/rot_force.png - nodes/ML17_eval/ForceDecomposition_3/trans_force.png - nodes/ML17_eval/ForceDecomposition_3/vib_force.png + ML17_eval_ForceDecomposition_4: + cmd: zntrack run ipsuite.nodes.ForceDecomposition --name ML17_eval_ForceDecomposition_4 + deps: + - nodes/ML17_eval/Prediction_4/atoms.h5 + - nodes/ML17_eval/Prediction_4/node-meta.json + metrics: + - nodes/ML17_eval/ForceDecomposition_4/node-meta.json: + cache: false + - nodes/ML17_eval/ForceDecomposition_4/rot_forces.json: + cache: false + - nodes/ML17_eval/ForceDecomposition_4/trans_forces.json: + cache: false + - nodes/ML17_eval/ForceDecomposition_4/vib_forces.json: + cache: false + - nodes/ML17_eval/ForceDecomposition_4/wasserstein_distance.json: + cache: false + outs: + - nodes/ML17_eval/ForceDecomposition_4/histogram.png + - nodes/ML17_eval/ForceDecomposition_4/rot_force.png + - nodes/ML17_eval/ForceDecomposition_4/trans_force.png + - nodes/ML17_eval/ForceDecomposition_4/vib_force.png ML17_eval_ForcesHistogram: cmd: zntrack run ipsuite.nodes.ForcesHistogram --name ML17_eval_ForcesHistogram deps: @@ -2969,6 +2998,31 @@ stages: - nodes/ML17_eval/PredictionMetrics_3/stress_deviatoric_df.csv - nodes/ML17_eval/PredictionMetrics_3/stress_df.csv - nodes/ML17_eval/PredictionMetrics_3/stress_hydrostatic_df.csv + ML17_eval_PredictionMetrics_4: + cmd: zntrack run ipsuite.nodes.PredictionMetrics --name ML17_eval_PredictionMetrics_4 + deps: + - nodes/ML17_eval/Prediction_4/atoms.h5 + - nodes/ML17_eval/Prediction_4/node-meta.json + metrics: + - nodes/ML17_eval/PredictionMetrics_4/deviat_stress.json: + cache: false + - nodes/ML17_eval/PredictionMetrics_4/energy.json: + cache: false + - nodes/ML17_eval/PredictionMetrics_4/forces.json: + cache: false + - nodes/ML17_eval/PredictionMetrics_4/hydro_stress.json: + cache: false + - nodes/ML17_eval/PredictionMetrics_4/node-meta.json: + cache: false + - nodes/ML17_eval/PredictionMetrics_4/stress.json: + cache: false + outs: + - nodes/ML17_eval/PredictionMetrics_4/energy_df.csv + - nodes/ML17_eval/PredictionMetrics_4/forces_df.csv + - nodes/ML17_eval/PredictionMetrics_4/plots + - nodes/ML17_eval/PredictionMetrics_4/stress_deviatoric_df.csv + - nodes/ML17_eval/PredictionMetrics_4/stress_df.csv + - nodes/ML17_eval/PredictionMetrics_4/stress_hydrostatic_df.csv ML17_eval_Prediction_1: cmd: zntrack run ipsuite.nodes.Prediction --name ML17_eval_Prediction_1 deps: @@ -3017,6 +3071,22 @@ stages: cache: false outs: - nodes/ML17_eval/Prediction_3/atoms.h5 + ML17_eval_Prediction_4: + cmd: zntrack run ipsuite.nodes.Prediction --name ML17_eval_Prediction_4 + deps: + - nodes/ML17_datasets/TorchD3_3/atoms.h5 + - nodes/ML17_datasets/TorchD3_3/node-meta.json + - nodes/ML17_training/MLModel_4/apax_model + - nodes/ML17_training/MLModel_4/log.csv + - nodes/ML17_training/MLModel_4/metrics.json + - nodes/ML17_training/MLModel_4/node-meta.json + - nodes/ML17_training/MLModel_4/train_atoms.extxyz + - nodes/ML17_training/MLModel_4/val_atoms.extxyz + metrics: + - nodes/ML17_eval/Prediction_4/node-meta.json: + cache: false + outs: + - nodes/ML17_eval/Prediction_4/atoms.h5 ML17_sampling_ASEGeoOpt: cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name ML17_sampling_ASEGeoOpt deps: @@ -3243,7 +3313,7 @@ stages: - nodes/ML17_training/MLModel/val_atoms.extxyz params: - ML17_training_MLModel - - config/ml17_ensemble.yaml: + - config/ml17_ensemble.yaml: null ML17_training_MLModel_1: cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_1 deps: @@ -3263,7 +3333,7 @@ stages: - nodes/ML17_training/MLModel_1/val_atoms.extxyz params: - ML17_training_MLModel_1 - - config/ml17_ensemble.yaml: + - config/ml17_ensemble.yaml: null ML17_training_MLModel_2: cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_2 deps: @@ -3283,7 +3353,7 @@ stages: - nodes/ML17_training/MLModel_2/val_atoms.extxyz params: - ML17_training_MLModel_2 - - config/ml17_ensemble_long_cutoff.yaml: + - config/ml17_ensemble_long_cutoff.yaml: null ML17_training_MLModel_3: cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_3 deps: @@ -3303,7 +3373,27 @@ stages: - nodes/ML17_training/MLModel_3/val_atoms.extxyz params: - ML17_training_MLModel_3 - - config/ml17_ensemble.yaml: + - config/ml17_ensemble.yaml: null + ML17_training_MLModel_4: + cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_4 + deps: + - nodes/ML17_datasets/TorchD3/atoms.h5 + - nodes/ML17_datasets/TorchD3/node-meta.json + - nodes/ML17_datasets/TorchD3_1/atoms.h5 + - nodes/ML17_datasets/TorchD3_1/node-meta.json + metrics: + - nodes/ML17_training/MLModel_4/metrics.json: + cache: false + - nodes/ML17_training/MLModel_4/node-meta.json: + cache: false + outs: + - nodes/ML17_training/MLModel_4/apax_model + - nodes/ML17_training/MLModel_4/log.csv + - nodes/ML17_training/MLModel_4/train_atoms.extxyz + - nodes/ML17_training/MLModel_4/val_atoms.extxyz + params: + - ML17_training_MLModel_4 + - config/ml17.yaml: null ML1_ASEGeoOpt: cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name ML1_ASEGeoOpt deps: @@ -3368,7 +3458,7 @@ 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: @@ -3473,7 +3563,7 @@ 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: @@ -3582,7 +3672,7 @@ 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: @@ -3699,7 +3789,7 @@ 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: @@ -3808,7 +3898,7 @@ 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: @@ -3937,7 +4027,7 @@ 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: @@ -4046,7 +4136,7 @@ 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: @@ -4187,7 +4277,7 @@ 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: @@ -4297,7 +4387,7 @@ 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: @@ -4450,7 +4540,7 @@ 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: @@ -4560,7 +4650,7 @@ 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: @@ -4725,7 +4815,7 @@ 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: @@ -4835,7 +4925,7 @@ 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: @@ -5012,7 +5102,7 @@ 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: @@ -5122,7 +5212,7 @@ 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: @@ -5311,7 +5401,7 @@ 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: @@ -5421,7 +5511,7 @@ 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: @@ -5622,7 +5712,7 @@ 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: @@ -5907,7 +5997,7 @@ 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: @@ -6124,7 +6214,7 @@ 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: @@ -6219,7 +6309,7 @@ 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: @@ -6330,7 +6420,7 @@ 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: @@ -6393,7 +6483,7 @@ stages: - nodes/d3_models/MLModel/val_atoms.extxyz params: - d3_models_MLModel - - config/final.yaml: + - config/final.yaml: null d3_models_MLModel_1: cmd: zntrack run ipsuite.nodes.Apax --name d3_models_MLModel_1 deps: @@ -6413,7 +6503,152 @@ stages: - nodes/d3_models/MLModel_1/val_atoms.extxyz params: - d3_models_MLModel_1 - - config/final.yaml: + - config/final.yaml: null + depl_ASEGeoOpt: + cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt + deps: + - nodes/ML17_training/MLModel_1/apax_model + - nodes/ML17_training/MLModel_1/log.csv + - nodes/ML17_training/MLModel_1/metrics.json + - nodes/ML17_training/MLModel_1/node-meta.json + - nodes/ML17_training/MLModel_1/train_atoms.extxyz + - nodes/ML17_training/MLModel_1/val_atoms.extxyz + - nodes/depl/Packmol_1/atoms.h5 + - nodes/depl/Packmol_1/node-meta.json + - nodes/depl/Packmol_1/packmol + metrics: + - nodes/depl/ASEGeoOpt/node-meta.json: + cache: false + outs: + - nodes/depl/ASEGeoOpt/model_outs + - nodes/depl/ASEGeoOpt/trajectory.h5 + params: + - depl_ASEGeoOpt + depl_ASEMD: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD + deps: + - nodes/ML17_training/MLModel_1/apax_model + - nodes/ML17_training/MLModel_1/log.csv + - nodes/ML17_training/MLModel_1/metrics.json + - nodes/ML17_training/MLModel_1/node-meta.json + - nodes/ML17_training/MLModel_1/train_atoms.extxyz + - nodes/ML17_training/MLModel_1/val_atoms.extxyz + - nodes/depl/ASEGeoOpt/model_outs + - nodes/depl/ASEGeoOpt/node-meta.json + - nodes/depl/ASEGeoOpt/trajectory.h5 + metrics: + - nodes/depl/ASEMD/node-meta.json: + cache: false + - nodes/depl/ASEMD/steps_before_stopping.json: + cache: false + outs: + - nodes/depl/ASEMD/metrics_dict.csv + - nodes/depl/ASEMD/model + - nodes/depl/ASEMD/trajectory.h5 + params: + - depl_ASEMD + - depl_ASEMD+modifier+0 + - depl_ASEMD+thermostat + depl_ASEMD_1: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1 + deps: + - nodes/ML17_training/MLModel_1/apax_model + - nodes/ML17_training/MLModel_1/log.csv + - nodes/ML17_training/MLModel_1/metrics.json + - nodes/ML17_training/MLModel_1/node-meta.json + - nodes/ML17_training/MLModel_1/train_atoms.extxyz + - nodes/ML17_training/MLModel_1/val_atoms.extxyz + - nodes/depl/ASEMD/metrics_dict.csv + - nodes/depl/ASEMD/model + - nodes/depl/ASEMD/node-meta.json + - nodes/depl/ASEMD/steps_before_stopping.json + - nodes/depl/ASEMD/trajectory.h5 + metrics: + - nodes/depl/ASEMD_1/node-meta.json: + cache: false + - nodes/depl/ASEMD_1/steps_before_stopping.json: + cache: false + outs: + - nodes/depl/ASEMD_1/metrics_dict.csv + - nodes/depl/ASEMD_1/model + - nodes/depl/ASEMD_1/trajectory.h5 + params: + - depl_ASEMD_1 + - depl_ASEMD_1+thermostat + depl_ApaxJaxMD: + cmd: zntrack run ipsuite.nodes.ApaxJaxMD --name depl_ApaxJaxMD + deps: + - nodes/ML17_training/MLModel_1/apax_model + - nodes/ML17_training/MLModel_1/log.csv + - nodes/ML17_training/MLModel_1/metrics.json + - nodes/ML17_training/MLModel_1/node-meta.json + - nodes/ML17_training/MLModel_1/train_atoms.extxyz + - nodes/ML17_training/MLModel_1/val_atoms.extxyz + - nodes/depl/ASEMD_1/metrics_dict.csv + - nodes/depl/ASEMD_1/model + - nodes/depl/ASEMD_1/node-meta.json + - nodes/depl/ASEMD_1/steps_before_stopping.json + - nodes/depl/ASEMD_1/trajectory.h5 + metrics: + - nodes/depl/ApaxJaxMD/node-meta.json: + cache: false + outs: + - nodes/depl/ApaxJaxMD/initial_structure.extxyz + - nodes/depl/ApaxJaxMD/md + params: + - depl_ApaxJaxMD + - config/md.yaml: null + depl_Packmol: + cmd: zntrack run ipsuite.nodes.Packmol --name depl_Packmol + deps: + - nodes/depl/SmilesToAtoms/atoms.h5 + - nodes/depl/SmilesToAtoms/molecule.png + - nodes/depl/SmilesToAtoms/node-meta.json + - nodes/depl/SmilesToAtoms_1/atoms.h5 + - nodes/depl/SmilesToAtoms_1/molecule.png + - nodes/depl/SmilesToAtoms_1/node-meta.json + metrics: + - nodes/depl/Packmol/node-meta.json: + cache: false + outs: + - nodes/depl/Packmol/atoms.h5 + - nodes/depl/Packmol/packmol + params: + - depl_Packmol + depl_Packmol_1: + cmd: zntrack run ipsuite.nodes.Packmol --name depl_Packmol_1 + deps: + - nodes/depl/Packmol/atoms.h5 + - nodes/depl/Packmol/node-meta.json + - nodes/depl/Packmol/packmol + metrics: + - nodes/depl/Packmol_1/node-meta.json: + cache: false + outs: + - nodes/depl/Packmol_1/atoms.h5 + - nodes/depl/Packmol_1/packmol + params: + - depl_Packmol_1 + depl_SmilesToAtoms: + cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name depl_SmilesToAtoms + metrics: + - nodes/depl/SmilesToAtoms/node-meta.json: + cache: false + outs: + - nodes/depl/SmilesToAtoms/atoms.h5 + - nodes/depl/SmilesToAtoms/molecule.png + params: + - depl_SmilesToAtoms + depl_SmilesToAtoms_1: + cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name depl_SmilesToAtoms_1 + metrics: + - nodes/depl/SmilesToAtoms_1/node-meta.json: + cache: false + outs: + - nodes/depl/SmilesToAtoms_1/atoms.h5 + - nodes/depl/SmilesToAtoms_1/molecule.png + params: + - depl_SmilesToAtoms_1 final_MLModel: cmd: zntrack run ipsuite.nodes.Apax --name final_MLModel deps: @@ -6486,7 +6721,7 @@ 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: @@ -6601,7 +6836,7 @@ 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: @@ -6855,7 +7090,7 @@ stages: - nodes/wo_d3/CP2KSinglePoint/atoms.h5 - nodes/wo_d3/CP2KSinglePoint/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null wo_d3_CP2KSinglePoint_1: cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name wo_d3_CP2KSinglePoint_1 deps: @@ -6871,7 +7106,7 @@ stages: - nodes/wo_d3/CP2KSinglePoint_1/atoms.h5 - nodes/wo_d3/CP2KSinglePoint_1/cp2k params: - - config/cp2k_wo_d3.yaml: + - config/cp2k_wo_d3.yaml: null wo_d3_MLModel: cmd: zntrack run ipsuite.nodes.Apax --name wo_d3_MLModel deps: @@ -6893,7 +7128,7 @@ stages: - nodes/wo_d3/MLModel/val_atoms.extxyz params: - wo_d3_MLModel - - config/final.yaml: + - config/final.yaml: null wo_d3_model_MLModel: cmd: zntrack run ipsuite.nodes.Apax --name wo_d3_model_MLModel deps: @@ -6915,4 +7150,4 @@ stages: - nodes/wo_d3_model/MLModel/val_atoms.extxyz params: - wo_d3_model_MLModel - - config/final.yaml: + - config/final.yaml: null diff --git a/env.yaml b/env.yaml new file mode 100644 index 0000000..1bf5f61 --- /dev/null +++ b/env.yaml @@ -0,0 +1,2 @@ +global: + XLA_FLAGS: "--xla_gpu_enable_triton_softmax_fusion=true --xla_gpu_triton_gemm_any=True --xla_gpu_enable_async_collectives=true --xla_gpu_enable_latency_hiding_scheduler=true --xla_gpu_enable_highest_priority_async_stream=true" \ No newline at end of file diff --git a/main.py b/main.py index 77cdc74..f83bb13 100644 --- a/main.py +++ b/main.py @@ -898,6 +898,12 @@ config="config/ml17_ensemble.yaml", ) + model_single = ips.models.Apax( + data=train_d3_short, + validation_data=val_d3_short, + config="config/ml17.yaml", + ) + with project.group("ML17_eval") as ml17_eval: ips.analysis.EnergyHistogram(data=train_data_nod3, bins=100) @@ -923,6 +929,75 @@ metrics = ips.analysis.PredictionMetrics(data=prediction) ips.analysis.ForceDecomposition(data=prediction) - + prediction = ips.analysis.Prediction(data=val_d3_medium, model=model_single) + metrics = ips.analysis.PredictionMetrics(data=prediction) + ips.analysis.ForceDecomposition(data=prediction) + + +ramp_density = ips.calculators.RescaleBoxModifier( + density=1204 +) +thermostat = ips.calculators.LangevinThermostat( + temperature=293, friction=0.01, time_step=0.5 +) +# https://pubs.acs.org/doi/10.1021/jp306146s + +with project.group("depl") as depl: + anion = ips.configuration_generation.SmilesToAtoms( + smiles="[B-](F)(F)(F)F" + ) + cation = ips.configuration_generation.SmilesToAtoms( + smiles="CCCCN1C=C[N+](=C1)C" + ) + + single_structure = ips.configuration_generation.Packmol( + data=[cation.atoms, anion.atoms], + count=[1, 1], + density=1210, + pbc=False, + ) + + structure = ips.configuration_generation.Packmol( + data=[single_structure.atoms], + count=[16], # 16, 32, 64 + density=900, + ) + + geo_opt = ips.calculators.ASEGeoOpt( + model=model_short, + data=structure.atoms, + data_id=-1, + optimizer="FIRE", + run_kwargs={"fmax": 0.05}, + ) + + density_md = ips.calculators.ASEMD( + data=geo_opt.atoms, + data_id=-1, + model=model_short, + modifier=[ramp_density], + thermostat=thermostat, + steps=10_000, + sampling_rate=10, + ) + + # relaxation + + md = ips.calculators.ASEMD( + data=density_md.atoms, + data_id=-1, + model=model_short, + thermostat=thermostat, + steps=10_000, + sampling_rate=10, + use_momenta=True, + ) + + md = ips.calculators.ApaxJaxMD( + data=md.atoms, + data_id=-1, + model=model_short, + md_parameter_file="config/md.yaml", + ) -project.build(nodes=[ml17_data, ml17_train, ml17_eval]) +project.build(nodes=[depl]) diff --git a/nodes/ML17_eval/ForceDecomposition_4/.gitignore b/nodes/ML17_eval/ForceDecomposition_4/.gitignore new file mode 100644 index 0000000..04c4fc2 --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/.gitignore @@ -0,0 +1,4 @@ +/histogram.png +/trans_force.png +/vib_force.png +/rot_force.png diff --git a/nodes/ML17_eval/ForceDecomposition_4/node-meta.json b/nodes/ML17_eval/ForceDecomposition_4/node-meta.json new file mode 100644 index 0000000..aacfa66 --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/node-meta.json @@ -0,0 +1 @@ +{"uuid": "9d3ccd0e-b33e-4c92-a1ce-49c79f64aa5f"} \ No newline at end of file diff --git a/nodes/ML17_eval/ForceDecomposition_4/rot_forces.json b/nodes/ML17_eval/ForceDecomposition_4/rot_forces.json new file mode 100644 index 0000000..7a2530c --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/rot_forces.json @@ -0,0 +1,8 @@ +{ + "rmse": 40.35920542582403, + "mse": 1628.865462603864, + "mae": 12.999871012488015, + "max": 452.09189038357323, + "lp4": 0.023975823684521398, + "rrmse": 0.9204805884935616 +} \ No newline at end of file diff --git a/nodes/ML17_eval/ForceDecomposition_4/trans_forces.json b/nodes/ML17_eval/ForceDecomposition_4/trans_forces.json new file mode 100644 index 0000000..ccfa325 --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/trans_forces.json @@ -0,0 +1,8 @@ +{ + "rmse": 36.30414622189521, + "mse": 1317.991032900748, + "mae": 13.318907989050325, + "max": 290.34897890258435, + "lp4": 0.019723625529233502, + "rrmse": 0.8945319907838492 +} \ No newline at end of file diff --git a/nodes/ML17_eval/ForceDecomposition_4/vib_forces.json b/nodes/ML17_eval/ForceDecomposition_4/vib_forces.json new file mode 100644 index 0000000..0184c43 --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/vib_forces.json @@ -0,0 +1,8 @@ +{ + "rmse": 68.01945061218659, + "mse": 4626.645661583691, + "mae": 41.70045978742288, + "max": 615.4068393453999, + "lp4": 0.032619732123514114, + "rrmse": 0.06504312736306475 +} \ No newline at end of file diff --git a/nodes/ML17_eval/ForceDecomposition_4/wasserstein_distance.json b/nodes/ML17_eval/ForceDecomposition_4/wasserstein_distance.json new file mode 100644 index 0000000..f5718a9 --- /dev/null +++ b/nodes/ML17_eval/ForceDecomposition_4/wasserstein_distance.json @@ -0,0 +1,22 @@ +{ + "all": { + "vib": 6.271446580489947e-07, + "rot": 0.00013457955520397807, + "trans": 0.00021274327429233835 + }, + "trans": { + "vib": 6.137575739382531e-07, + "rot": 0.00013310764839360003, + "trans": 0.0006018021465937603 + }, + "rot": { + "vib": 9.729891012818765e-07, + "rot": 0.00035366600211258976, + "trans": 0.00019107494111497475 + }, + "vib": { + "vib": 1.0015157097952206e-06, + "rot": 0.0001293824197226184, + "trans": 0.00021006547712469506 + } +} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/.gitignore b/nodes/ML17_eval/PredictionMetrics_4/.gitignore new file mode 100644 index 0000000..a78d9d9 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/.gitignore @@ -0,0 +1,6 @@ +/forces_df.csv +/plots +/stress_df.csv +/stress_deviatoric_df.csv +/stress_hydrostatic_df.csv +/energy_df.csv diff --git a/nodes/ML17_eval/PredictionMetrics_4/deviat_stress.json b/nodes/ML17_eval/PredictionMetrics_4/deviat_stress.json new file mode 100644 index 0000000..eaadde2 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/deviat_stress.json @@ -0,0 +1,8 @@ +{ + "rmse": 0.0001433632876742345, + "mse": 2.055303225276532e-08, + "mae": 0.000108539700892299, + "max": 0.0005809393887360771, + "lp4": 5.6925010003702e-07, + "rrmse": 0.054337250753307274 +} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/energy.json b/nodes/ML17_eval/PredictionMetrics_4/energy.json new file mode 100644 index 0000000..6aeba67 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/energy.json @@ -0,0 +1,8 @@ +{ + "rmse": 8.109785218111012, + "mse": 65.76861628389187, + "mae": 7.645091916628319, + "max": 11.245827799546532, + "lp4": 0.1272204026365948, + "rrmse": 0.4891562672303043 +} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/forces.json b/nodes/ML17_eval/PredictionMetrics_4/forces.json new file mode 100644 index 0000000..a3942fe --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/forces.json @@ -0,0 +1,8 @@ +{ + "rmse": 88.62395352922586, + "mse": 7854.205139150386, + "mae": 50.05099172236417, + "max": 668.30219573656, + "lp4": 0.03333438372316161, + "rrmse": 0.08669564211958092 +} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/hydro_stress.json b/nodes/ML17_eval/PredictionMetrics_4/hydro_stress.json new file mode 100644 index 0000000..c8c1661 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/hydro_stress.json @@ -0,0 +1,8 @@ +{ + "rmse": 0.0012260585451590157, + "mse": 1.5032195561574423e-06, + "mae": 0.0011073618220001373, + "max": 0.0018894251145553966, + "lp4": 1.984625814624385e-05, + "rrmse": 0.09631394534358707 +} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/node-meta.json b/nodes/ML17_eval/PredictionMetrics_4/node-meta.json new file mode 100644 index 0000000..d5fbd75 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/node-meta.json @@ -0,0 +1 @@ +{"uuid": "65fa4cb6-a945-4e05-b483-cdd7d3b9af59"} \ No newline at end of file diff --git a/nodes/ML17_eval/PredictionMetrics_4/stress.json b/nodes/ML17_eval/PredictionMetrics_4/stress.json new file mode 100644 index 0000000..10a8254 --- /dev/null +++ b/nodes/ML17_eval/PredictionMetrics_4/stress.json @@ -0,0 +1,8 @@ +{ + "rmse": 0.0007222369539414191, + "mse": 5.216262176385795e-07, + "mae": 0.0004361909776807074, + "max": 0.0024268598523759233, + "lp4": 2.9713363260546545e-06, + "rrmse": 0.0851399572375242 +} \ No newline at end of file diff --git a/nodes/ML17_eval/Prediction_4/.gitignore b/nodes/ML17_eval/Prediction_4/.gitignore new file mode 100644 index 0000000..588760b --- /dev/null +++ b/nodes/ML17_eval/Prediction_4/.gitignore @@ -0,0 +1 @@ +/atoms.h5 diff --git a/nodes/ML17_eval/Prediction_4/node-meta.json b/nodes/ML17_eval/Prediction_4/node-meta.json new file mode 100644 index 0000000..8a30983 --- /dev/null +++ b/nodes/ML17_eval/Prediction_4/node-meta.json @@ -0,0 +1 @@ +{"uuid": "43973942-75ef-4de8-8bca-66de0680fa86"} \ No newline at end of file diff --git a/nodes/ML17_training/MLModel_4/.gitignore b/nodes/ML17_training/MLModel_4/.gitignore new file mode 100644 index 0000000..9c0fb99 --- /dev/null +++ b/nodes/ML17_training/MLModel_4/.gitignore @@ -0,0 +1,4 @@ +/train_atoms.extxyz +/val_atoms.extxyz +/apax_model +/log.csv diff --git a/nodes/ML17_training/MLModel_4/metrics.json b/nodes/ML17_training/MLModel_4/metrics.json new file mode 100644 index 0000000..7756d33 --- /dev/null +++ b/nodes/ML17_training/MLModel_4/metrics.json @@ -0,0 +1,12 @@ +{ + "epoch": 430.0, + "epoch_time": 6.570879936218262, + "train_energy_mae": 1.9981157914131435, + "train_forces_mae": 0.0430163158399187, + "train_loss": 0.053235354636869, + "train_stress_mae": 5.701792904231977, + "val_energy_mae": 0.920879534910013, + "val_forces_mae": 0.058694560749805, + "val_loss": 0.1382012981764417, + "val_stress_mae": 6.655455032587216 +} \ No newline at end of file diff --git a/nodes/ML17_training/MLModel_4/node-meta.json b/nodes/ML17_training/MLModel_4/node-meta.json new file mode 100644 index 0000000..fa73f5e --- /dev/null +++ b/nodes/ML17_training/MLModel_4/node-meta.json @@ -0,0 +1 @@ +{"uuid": "5279bc24-f186-4c0c-9025-47571680c60a"} \ No newline at end of file diff --git a/nodes/depl/ASEGeoOpt/.gitignore b/nodes/depl/ASEGeoOpt/.gitignore new file mode 100644 index 0000000..e8c98e8 --- /dev/null +++ b/nodes/depl/ASEGeoOpt/.gitignore @@ -0,0 +1,2 @@ +/model_outs +/trajectory.h5 diff --git a/nodes/depl/ASEGeoOpt/node-meta.json b/nodes/depl/ASEGeoOpt/node-meta.json new file mode 100644 index 0000000..b49e633 --- /dev/null +++ b/nodes/depl/ASEGeoOpt/node-meta.json @@ -0,0 +1 @@ +{"uuid": "0d584356-51f5-4a5f-ace8-5a4c3eaacc1f"} \ No newline at end of file diff --git a/nodes/depl/ASEMD/.gitignore b/nodes/depl/ASEMD/.gitignore new file mode 100644 index 0000000..6673390 --- /dev/null +++ b/nodes/depl/ASEMD/.gitignore @@ -0,0 +1,3 @@ +/model +/metrics_dict.csv +/trajectory.h5 diff --git a/nodes/depl/ASEMD/node-meta.json b/nodes/depl/ASEMD/node-meta.json new file mode 100644 index 0000000..49bd4fa --- /dev/null +++ b/nodes/depl/ASEMD/node-meta.json @@ -0,0 +1 @@ +{"uuid": "5cdcbcd3-d5bd-4f53-ac68-784f7cebab59", "run_count": 1} \ No newline at end of file diff --git a/nodes/depl/ASEMD/steps_before_stopping.json b/nodes/depl/ASEMD/steps_before_stopping.json new file mode 100644 index 0000000..d7d17fc --- /dev/null +++ b/nodes/depl/ASEMD/steps_before_stopping.json @@ -0,0 +1 @@ +-1 \ No newline at end of file diff --git a/nodes/depl/ASEMD_1/.gitignore b/nodes/depl/ASEMD_1/.gitignore new file mode 100644 index 0000000..6673390 --- /dev/null +++ b/nodes/depl/ASEMD_1/.gitignore @@ -0,0 +1,3 @@ +/model +/metrics_dict.csv +/trajectory.h5 diff --git a/nodes/depl/ASEMD_1/node-meta.json b/nodes/depl/ASEMD_1/node-meta.json new file mode 100644 index 0000000..b63485f --- /dev/null +++ b/nodes/depl/ASEMD_1/node-meta.json @@ -0,0 +1 @@ +{"uuid": "636c3ae9-1574-48e7-b538-c7f4b22ad9e6", "run_count": 1} \ No newline at end of file diff --git a/nodes/depl/ASEMD_1/steps_before_stopping.json b/nodes/depl/ASEMD_1/steps_before_stopping.json new file mode 100644 index 0000000..d7d17fc --- /dev/null +++ b/nodes/depl/ASEMD_1/steps_before_stopping.json @@ -0,0 +1 @@ +-1 \ No newline at end of file diff --git a/nodes/depl/ApaxJaxMD/.gitignore b/nodes/depl/ApaxJaxMD/.gitignore new file mode 100644 index 0000000..6bca8fa --- /dev/null +++ b/nodes/depl/ApaxJaxMD/.gitignore @@ -0,0 +1,2 @@ +/initial_structure.extxyz +/md diff --git a/nodes/depl/ApaxJaxMD/node-meta.json b/nodes/depl/ApaxJaxMD/node-meta.json new file mode 100644 index 0000000..bc46e84 --- /dev/null +++ b/nodes/depl/ApaxJaxMD/node-meta.json @@ -0,0 +1 @@ +{"uuid": "d77a44fe-b51a-41fa-81fa-46715ffc4d92", "run_count": 3} \ No newline at end of file diff --git a/nodes/depl/Packmol/.gitignore b/nodes/depl/Packmol/.gitignore new file mode 100644 index 0000000..4d39e89 --- /dev/null +++ b/nodes/depl/Packmol/.gitignore @@ -0,0 +1,2 @@ +/atoms.h5 +/packmol diff --git a/nodes/depl/Packmol/node-meta.json b/nodes/depl/Packmol/node-meta.json new file mode 100644 index 0000000..c420b06 --- /dev/null +++ b/nodes/depl/Packmol/node-meta.json @@ -0,0 +1 @@ +{"uuid": "c1b8c707-89b9-444f-892d-2f173a8bad8d"} \ No newline at end of file diff --git a/nodes/depl/Packmol_1/.gitignore b/nodes/depl/Packmol_1/.gitignore new file mode 100644 index 0000000..4d39e89 --- /dev/null +++ b/nodes/depl/Packmol_1/.gitignore @@ -0,0 +1,2 @@ +/atoms.h5 +/packmol diff --git a/nodes/depl/Packmol_1/node-meta.json b/nodes/depl/Packmol_1/node-meta.json new file mode 100644 index 0000000..b1bd775 --- /dev/null +++ b/nodes/depl/Packmol_1/node-meta.json @@ -0,0 +1 @@ +{"uuid": "12b972d9-3c62-4873-a260-c2a25705c182"} \ No newline at end of file diff --git a/nodes/depl/SmilesToAtoms/.gitignore b/nodes/depl/SmilesToAtoms/.gitignore new file mode 100644 index 0000000..5d8cc59 --- /dev/null +++ b/nodes/depl/SmilesToAtoms/.gitignore @@ -0,0 +1,2 @@ +/molecule.png +/atoms.h5 diff --git a/nodes/depl/SmilesToAtoms/node-meta.json b/nodes/depl/SmilesToAtoms/node-meta.json new file mode 100644 index 0000000..d8e6a82 --- /dev/null +++ b/nodes/depl/SmilesToAtoms/node-meta.json @@ -0,0 +1 @@ +{"uuid": "2add615c-4a68-41ae-bdf5-573ece4f1835"} \ No newline at end of file diff --git a/nodes/depl/SmilesToAtoms_1/.gitignore b/nodes/depl/SmilesToAtoms_1/.gitignore new file mode 100644 index 0000000..5d8cc59 --- /dev/null +++ b/nodes/depl/SmilesToAtoms_1/.gitignore @@ -0,0 +1,2 @@ +/molecule.png +/atoms.h5 diff --git a/nodes/depl/SmilesToAtoms_1/node-meta.json b/nodes/depl/SmilesToAtoms_1/node-meta.json new file mode 100644 index 0000000..fc66e1f --- /dev/null +++ b/nodes/depl/SmilesToAtoms_1/node-meta.json @@ -0,0 +1 @@ +{"uuid": "08271b39-8b53-453b-85bb-9c15bb043eb5"} \ No newline at end of file diff --git a/params.yaml b/params.yaml index 76318bd..0481aaf 100644 --- a/params.yaml +++ b/params.yaml @@ -543,6 +543,11 @@ ML17_training_MLModel_3: use_energy: true use_forces: true use_stresses: false +ML17_training_MLModel_4: + jax_enable_x64: true + use_energy: true + use_forces: true + use_stresses: false ML1_ASEGeoOpt: data_id: -1 dump_rate: 1000 @@ -1227,6 +1232,85 @@ d3_models_MLModel_1: use_energy: true use_forces: true use_stresses: false +depl_ASEGeoOpt: + data_id: -1 + dump_rate: 1000 + init_kwargs: {} + optimizer: FIRE + repeat: + - 1 + - 1 + - 1 + run_kwargs: + fmax: 0.05 +depl_ASEMD: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 10000 + use_momenta: false + wrap: false +depl_ASEMD+modifier+0: + cell: null + density: 1204 +depl_ASEMD+thermostat: + friction: 0.01 + temperature: 293 + time_step: 0.5 +depl_ASEMD_1: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 10000 + use_momenta: true + wrap: false +depl_ASEMD_1+thermostat: + friction: 0.01 + temperature: 293 + time_step: 0.5 +depl_ApaxJaxMD: + data_id: -1 + md_parameter: null + repeat: null +depl_Packmol: + box: null + count: + - 1 + - 1 + data_ids: null + density: 1210 + pbc: false + tolerance: 2.0 +depl_Packmol_1: + box: null + count: + - 16 + data_ids: null + density: 900 + pbc: true + tolerance: 2.0 +depl_SmilesToAtoms: + cell: null + optimizer: UFF + seed: 1234 + smiles: '[B-](F)(F)(F)F' +depl_SmilesToAtoms_1: + cell: null + optimizer: UFF + seed: 1234 + smiles: CCCCN1C=C[N+](=C1)C final_MLModel: jax_enable_x64: true use_energy: true diff --git a/zntrack.json b/zntrack.json index c5d44eb..ece90ab 100644 --- a/zntrack.json +++ b/zntrack.json @@ -20178,6 +20178,64 @@ "value": "nodes/ML17_training/MLModel_3" } }, + "ML17_training_MLModel_4": { + "config": "config/ml17.yaml", + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "TorchD3", + "name": "ML17_datasets_TorchD3", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "metrics_epoch": { + "_type": "pathlib.Path", + "value": "$nwd$/log.csv" + }, + "model": null, + "model_directory": { + "_type": "pathlib.Path", + "value": "$nwd$/apax_model" + }, + "train_data_file": { + "_type": "pathlib.Path", + "value": "$nwd$/train_atoms.extxyz" + }, + "validation_data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "TorchD3", + "name": "ML17_datasets_TorchD3_1", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "validation_data_file": { + "_type": "pathlib.Path", + "value": "$nwd$/val_atoms.extxyz" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/ML17_training/MLModel_4" + } + }, "ML17_eval_EnergyHistogram": { "data": { "_type": "znflow.CombinedConnections", @@ -20510,6 +20568,7 @@ "_type": "pathlib.Path", "value": "$nwd$/plots" }, + "reference": null, "stress_deviatoric_df_file": { "_type": "pathlib.Path", "value": "$nwd$/stress_deviatoric_df.csv" @@ -20549,6 +20608,7 @@ "_type": "pathlib.Path", "value": "$nwd$/histogram.png" }, + "reference": null, "rot_force_plt": { "_type": "pathlib.Path", "value": "$nwd$/rot_force.png" @@ -20637,6 +20697,7 @@ "_type": "pathlib.Path", "value": "$nwd$/plots" }, + "reference": null, "stress_deviatoric_df_file": { "_type": "pathlib.Path", "value": "$nwd$/stress_deviatoric_df.csv" @@ -20676,6 +20737,7 @@ "_type": "pathlib.Path", "value": "$nwd$/histogram.png" }, + "reference": null, "rot_force_plt": { "_type": "pathlib.Path", "value": "$nwd$/rot_force.png" @@ -20764,6 +20826,7 @@ "_type": "pathlib.Path", "value": "$nwd$/plots" }, + "reference": null, "stress_deviatoric_df_file": { "_type": "pathlib.Path", "value": "$nwd$/stress_deviatoric_df.csv" @@ -20803,6 +20866,7 @@ "_type": "pathlib.Path", "value": "$nwd$/histogram.png" }, + "reference": null, "rot_force_plt": { "_type": "pathlib.Path", "value": "$nwd$/rot_force.png" @@ -20891,6 +20955,7 @@ "_type": "pathlib.Path", "value": "$nwd$/plots" }, + "reference": null, "stress_deviatoric_df_file": { "_type": "pathlib.Path", "value": "$nwd$/stress_deviatoric_df.csv" @@ -20930,6 +20995,7 @@ "_type": "pathlib.Path", "value": "$nwd$/histogram.png" }, + "reference": null, "rot_force_plt": { "_type": "pathlib.Path", "value": "$nwd$/rot_force.png" @@ -20946,5 +21012,483 @@ "_type": "pathlib.Path", "value": "nodes/ML17_eval/ForceDecomposition_3" } + }, + "ML17_eval_Prediction_4": { + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "TorchD3", + "name": "ML17_datasets_TorchD3_3", + "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": "Apax", + "name": "ML17_training_MLModel_4", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/ML17_eval/Prediction_4" + } + }, + "ML17_eval_PredictionMetrics_4": { + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "Prediction", + "name": "ML17_eval_Prediction_4", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "energy_df_file": { + "_type": "pathlib.Path", + "value": "$nwd$/energy_df.csv" + }, + "forces_df_file": { + "_type": "pathlib.Path", + "value": "$nwd$/forces_df.csv" + }, + "plots_dir": { + "_type": "pathlib.Path", + "value": "$nwd$/plots" + }, + "reference": null, + "stress_deviatoric_df_file": { + "_type": "pathlib.Path", + "value": "$nwd$/stress_deviatoric_df.csv" + }, + "stress_df_file": { + "_type": "pathlib.Path", + "value": "$nwd$/stress_df.csv" + }, + "stress_hydrostatic_df_file": { + "_type": "pathlib.Path", + "value": "$nwd$/stress_hydrostatic_df.csv" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/ML17_eval/PredictionMetrics_4" + } + }, + "ML17_eval_ForceDecomposition_4": { + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "Prediction", + "name": "ML17_eval_Prediction_4", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "histogram_plt": { + "_type": "pathlib.Path", + "value": "$nwd$/histogram.png" + }, + "reference": null, + "rot_force_plt": { + "_type": "pathlib.Path", + "value": "$nwd$/rot_force.png" + }, + "trans_force_plt": { + "_type": "pathlib.Path", + "value": "$nwd$/trans_force.png" + }, + "vib_force_plt": { + "_type": "pathlib.Path", + "value": "$nwd$/vib_force.png" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/ML17_eval/ForceDecomposition_4" + } + }, + "depl_SmilesToAtoms": { + "image": { + "_type": "pathlib.Path", + "value": "$nwd$/molecule.png" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/SmilesToAtoms" + } + }, + "depl_SmilesToAtoms_1": { + "image": { + "_type": "pathlib.Path", + "value": "$nwd$/molecule.png" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/SmilesToAtoms_1" + } + }, + "depl_Packmol": { + "data": [ + { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "SmilesToAtoms", + "name": "depl_SmilesToAtoms_1", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "SmilesToAtoms", + "name": "depl_SmilesToAtoms", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + } + ], + "structures": { + "_type": "pathlib.Path", + "value": "$nwd$/packmol" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/Packmol" + } + }, + "depl_Packmol_1": { + "data": [ + { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "Packmol", + "name": "depl_Packmol", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + } + ], + "structures": { + "_type": "pathlib.Path", + "value": "$nwd$/packmol" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/Packmol_1" + } + }, + "depl_ASEGeoOpt": { + "checker_list": null, + "constraint_list": null, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "Packmol", + "name": "depl_Packmol_1", + "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": "Apax", + "name": "ML17_training_MLModel_1", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "model_outs": { + "_type": "pathlib.Path", + "value": "$nwd$/model_outs" + }, + "traj_file": { + "_type": "pathlib.Path", + "value": "$nwd$/trajectory.h5" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/ASEGeoOpt" + } + }, + "depl_ASEMD": { + "checker_list": null, + "constraint_list": null, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "ASEGeoOpt", + "name": "depl_ASEGeoOpt", + "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": "Apax", + "name": "ML17_training_MLModel_1", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "model_outs": { + "_type": "pathlib.Path", + "value": "$nwd$/model" + }, + "modifier": [ + { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "RescaleBoxModifier", + "name": "depl_ASEMD+modifier+0", + "remote": null, + "rev": null + } + } + ], + "thermostat": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "LangevinThermostat", + "name": "depl_ASEMD+thermostat", + "remote": null, + "rev": null + } + }, + "traj_file": { + "_type": "pathlib.Path", + "value": "$nwd$/trajectory.h5" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/ASEMD" + } + }, + "depl_ASEMD+modifier+0": { + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl_ASEMD+modifier+0" + } + }, + "depl_ASEMD+thermostat": { + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl_ASEMD+thermostat" + } + }, + "depl_ASEMD_1": { + "checker_list": null, + "constraint_list": null, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "ASEMD", + "name": "depl_ASEMD", + "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": "Apax", + "name": "ML17_training_MLModel_1", + "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": "LangevinThermostat", + "name": "depl_ASEMD_1+thermostat", + "remote": null, + "rev": null + } + }, + "traj_file": { + "_type": "pathlib.Path", + "value": "$nwd$/trajectory.h5" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/ASEMD_1" + } + }, + "depl_ASEMD_1+thermostat": { + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl_ASEMD_1+thermostat" + } + }, + "depl_ApaxJaxMD": { + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "ASEMD", + "name": "depl_ASEMD_1", + "remote": null, + "rev": null + } + }, + "attribute": "atoms", + "item": null + } + }, + "data_file": null, + "init_struc_dir": { + "_type": "pathlib.Path", + "value": "$nwd$/initial_structure.extxyz" + }, + "md_parameter_file": "config/md.yaml", + "model": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": "ipsuite.nodes", + "cls": "Apax", + "name": "ML17_training_MLModel_1", + "remote": null, + "rev": null + } + }, + "attribute": null, + "item": null + } + }, + "sim_dir": { + "_type": "pathlib.Path", + "value": "$nwd$/md" + }, + "nwd": { + "_type": "pathlib.Path", + "value": "nodes/depl/ApaxJaxMD" + } } } \ No newline at end of file