diff --git a/config/final.yaml b/config/final.yaml index 6b09b65..8d2a08e 100644 --- a/config/final.yaml +++ b/config/final.yaml @@ -33,7 +33,7 @@ model: nn: - 512 - 512 - r_max: 5.5 + r_max: 6.0 r_min: 0.7 b_init: zeros diff --git a/dvc.lock b/dvc.lock index 78c792b..cbfcac9 100644 --- a/dvc.lock +++ b/dvc.lock @@ -422,7 +422,7 @@ stages: nn: - 512 - 512 - r_max: 5.5 + r_max: 6.0 r_min: 0.7 b_init: zeros emb_init: uniform @@ -444,20 +444,20 @@ stages: outs: - path: nodes/final/MLModel/apax_model hash: md5 - md5: 4669bd38d8935f67fdb04e35dfe89ee6.dir + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir size: 42264512 nfiles: 6 - path: nodes/final/MLModel/log.csv hash: md5 - md5: b5cb6ea431ab82fe943b46d2a4f2c0a9 - size: 354566 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 - path: nodes/final/MLModel/metrics.json hash: md5 - md5: ff45effc5f0dcd0293b5acdd3fbef710 + md5: b4469fcc555cdbfbe570d0aa4e40f14f size: 389 - path: nodes/final/MLModel/node-meta.json hash: md5 - md5: 3e9e775f8cf0cde94e88e871f6a6b985 + md5: 970951f390e6d7586cae686fdd9f6dda size: 48 - path: nodes/final/MLModel/train_atoms.extxyz hash: md5 @@ -484,20 +484,20 @@ stages: size: 44259 - path: nodes/final/MLModel/apax_model hash: md5 - md5: 4669bd38d8935f67fdb04e35dfe89ee6.dir + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir size: 42264512 nfiles: 6 - path: nodes/final/MLModel/log.csv hash: md5 - md5: b5cb6ea431ab82fe943b46d2a4f2c0a9 - size: 354566 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 - path: nodes/final/MLModel/metrics.json hash: md5 - md5: ff45effc5f0dcd0293b5acdd3fbef710 + md5: b4469fcc555cdbfbe570d0aa4e40f14f size: 389 - path: nodes/final/MLModel/node-meta.json hash: md5 - md5: 3e9e775f8cf0cde94e88e871f6a6b985 + md5: 970951f390e6d7586cae686fdd9f6dda size: 48 - path: nodes/final/MLModel/train_atoms.extxyz hash: md5 @@ -510,73 +510,73 @@ stages: outs: - path: nodes/final/Prediction/atoms.h5 hash: md5 - md5: b628f151b7bde3552a08c6a96ea774b1 + md5: 2d7e00e3c7638fde3b2afc31ccb4d392 size: 8722872 - path: nodes/final/Prediction/node-meta.json hash: md5 - md5: 3c46b02ee5da0d31658ef96879f720f5 + md5: a515f08d03255d896fe77df0de07c4bb size: 48 final_PredictionMetrics: cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_PredictionMetrics deps: - path: nodes/final/Prediction/atoms.h5 hash: md5 - md5: b628f151b7bde3552a08c6a96ea774b1 + md5: 2d7e00e3c7638fde3b2afc31ccb4d392 size: 8722872 - path: nodes/final/Prediction/node-meta.json hash: md5 - md5: 3c46b02ee5da0d31658ef96879f720f5 + md5: a515f08d03255d896fe77df0de07c4bb size: 48 outs: - path: nodes/final/PredictionMetrics/deviat_stress.json hash: md5 - md5: f3ddc9cd68bc405d78ea9d90b7766971 - size: 207 + md5: 184d6fd16699b04f75a18437a8e1d3a3 + size: 208 - path: nodes/final/PredictionMetrics/energy.json hash: md5 - md5: 63ca25f5b387ebca4426fcce87f04d0f - size: 190 + md5: 6e9bd5446d9bd63a65a69b9c96c3e0db + size: 191 - path: nodes/final/PredictionMetrics/energy_df.csv hash: md5 - md5: e0083fe2be7ff76795bf4d699411e96b - size: 21329 + md5: b2f3c68c60c17f66000cb4092d7ab89c + size: 21330 - path: nodes/final/PredictionMetrics/forces.json hash: md5 - md5: 264174a2eeb4655aa6abc4d73d10a2bb + md5: 18460df73ed741f68164c97c8cdc547c size: 189 - path: nodes/final/PredictionMetrics/forces_df.csv hash: md5 - md5: 78039586831c952d6ae08760fa191b04 - size: 22660585 + md5: 29c4893c329c336973c4640a2c54aa85 + size: 22660514 - path: nodes/final/PredictionMetrics/hydro_stress.json hash: md5 - md5: 4cab42ab2c2b1d5309cfc44eb04a545d - size: 206 + md5: f15c6a9706988bafdfd7c8524ef4ab57 + size: 208 - path: nodes/final/PredictionMetrics/node-meta.json hash: md5 - md5: b3169e1faacc77ee2cecbe489210c7d7 + md5: a56f2a487eb9501a06d9fd111f4b14aa size: 48 - path: nodes/final/PredictionMetrics/plots hash: md5 - md5: d45eb180d81ecb82796af8bfa54a5ee9.dir - size: 360731 + md5: 589d4fa2abc5cc0e57ff658eaf6a2d1b.dir + size: 364855 nfiles: 5 - path: nodes/final/PredictionMetrics/stress.json hash: md5 - md5: 6879e9b6421fce30e30a633da4a843f7 - size: 209 + md5: 5b8c75d38a7a263afb4eaecdacccf0c4 + size: 208 - path: nodes/final/PredictionMetrics/stress_deviatoric_df.csv hash: md5 - md5: d96c97e13b00d3612cb10a36e74d9565 - size: 212168 + md5: e0ff3a61ce441459dd8ff01148f6f660 + size: 212136 - path: nodes/final/PredictionMetrics/stress_df.csv hash: md5 - md5: 687dc7620c49078c2523bd5fa55d349e - size: 207683 + md5: 6475643403075ed421d33e37d47fa84c + size: 207654 - path: nodes/final/PredictionMetrics/stress_hydrostatic_df.csv hash: md5 - md5: 01a8255697eb26e44a0a61df986f50ff - size: 23508 + md5: 8d364b1d7518dcd4bb527b301bfe7069 + size: 23504 md_SmilesToAtoms: cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name md_SmilesToAtoms params: @@ -21337,3 +21337,522 @@ stages: hash: md5 md5: 0a366e37c5368c0f3d9888f5d26a5d13 size: 58176 + 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: + - 32 + data_ids: + density: 900 + pbc: true + tolerance: 2.0 + outs: + - path: nodes/depl/Packmol_1/atoms.h5 + hash: md5 + md5: 80dfb7849c6eb8699d73f89538a954ed + size: 58688 + - path: nodes/depl/Packmol_1/node-meta.json + hash: md5 + md5: d5bba7573525324cbb15a83d9921e9cd + size: 48 + - path: nodes/depl/Packmol_1/packmol + hash: md5 + md5: 47d3e803210f655e9d56a52c37a21c34.dir + size: 55734 + nfiles: 3 + depl_ASEGeoOpt: + cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt + deps: + - path: nodes/depl/Packmol_1/atoms.h5 + hash: md5 + md5: 80dfb7849c6eb8699d73f89538a954ed + size: 58688 + - path: nodes/depl/Packmol_1/node-meta.json + hash: md5 + md5: d5bba7573525324cbb15a83d9921e9cd + size: 48 + - path: nodes/depl/Packmol_1/packmol + hash: md5 + md5: 47d3e803210f655e9d56a52c37a21c34.dir + size: 55734 + nfiles: 3 + - path: nodes/final/MLModel/apax_model + hash: md5 + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir + size: 42264512 + nfiles: 6 + - path: nodes/final/MLModel/log.csv + hash: md5 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 + - path: nodes/final/MLModel/metrics.json + hash: md5 + md5: b4469fcc555cdbfbe570d0aa4e40f14f + size: 389 + - path: nodes/final/MLModel/node-meta.json + hash: md5 + md5: 970951f390e6d7586cae686fdd9f6dda + size: 48 + - path: nodes/final/MLModel/train_atoms.extxyz + hash: md5 + md5: c73f7ed92deedd952c59845bde00a0b0 + size: 48855065 + - path: nodes/final/MLModel/val_atoms.extxyz + hash: md5 + md5: 9eda8d89a8543dc151afc20daa607205 + size: 3188610 + 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: 291d8bfd0b060f3266fb810464227902 + size: 48 + - path: nodes/depl/ASEGeoOpt/trajectory.h5 + hash: md5 + md5: 1580e84ebc54f88029265c0aafea091c + size: 25103616 + depl_ASEMD: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD + deps: + - 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: 291d8bfd0b060f3266fb810464227902 + size: 48 + - path: nodes/depl/ASEGeoOpt/trajectory.h5 + hash: md5 + md5: 1580e84ebc54f88029265c0aafea091c + size: 25103616 + - path: nodes/final/MLModel/apax_model + hash: md5 + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir + size: 42264512 + nfiles: 6 + - path: nodes/final/MLModel/log.csv + hash: md5 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 + - path: nodes/final/MLModel/metrics.json + hash: md5 + md5: b4469fcc555cdbfbe570d0aa4e40f14f + size: 389 + - path: nodes/final/MLModel/node-meta.json + hash: md5 + md5: 970951f390e6d7586cae686fdd9f6dda + size: 48 + - path: nodes/final/MLModel/train_atoms.extxyz + hash: md5 + md5: c73f7ed92deedd952c59845bde00a0b0 + size: 48855065 + - path: nodes/final/MLModel/val_atoms.extxyz + hash: md5 + md5: 9eda8d89a8543dc151afc20daa607205 + size: 3188610 + 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: 1300 + depl_ASEMD+thermostat: + friction: 0.01 + temperature: 300 + time_step: 0.5 + outs: + - path: nodes/depl/ASEMD/metrics_dict.csv + hash: md5 + md5: 4c4d25332b01df7d3ecad60b677370ca + size: 41994 + - path: nodes/depl/ASEMD/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD/node-meta.json + hash: md5 + md5: 09fa509712e5046c3ea180ad6741bc56 + size: 48 + - path: nodes/depl/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD/trajectory.h5 + hash: md5 + md5: 693b764f36458275f7da66a76c0550ad + size: 77719024 + depl_ASEMD_1: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1 + deps: + - path: nodes/depl/ASEMD/metrics_dict.csv + hash: md5 + md5: 4c4d25332b01df7d3ecad60b677370ca + size: 41994 + - path: nodes/depl/ASEMD/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD/node-meta.json + hash: md5 + md5: 09fa509712e5046c3ea180ad6741bc56 + size: 48 + - path: nodes/depl/ASEMD/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD/trajectory.h5 + hash: md5 + md5: 693b764f36458275f7da66a76c0550ad + size: 77719024 + - path: nodes/final/MLModel/apax_model + hash: md5 + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir + size: 42264512 + nfiles: 6 + - path: nodes/final/MLModel/log.csv + hash: md5 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 + - path: nodes/final/MLModel/metrics.json + hash: md5 + md5: b4469fcc555cdbfbe570d0aa4e40f14f + size: 389 + - path: nodes/final/MLModel/node-meta.json + hash: md5 + md5: 970951f390e6d7586cae686fdd9f6dda + size: 48 + - path: nodes/final/MLModel/train_atoms.extxyz + hash: md5 + md5: c73f7ed92deedd952c59845bde00a0b0 + size: 48855065 + - path: nodes/final/MLModel/val_atoms.extxyz + hash: md5 + md5: 9eda8d89a8543dc151afc20daa607205 + size: 3188610 + 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: 50000 + use_momenta: false + wrap: false + depl_ASEMD_1+thermostat: + friction: 0.01 + temperature: 300 + time_step: 0.5 + outs: + - path: nodes/depl/ASEMD_1/metrics_dict.csv + hash: md5 + md5: ae03c002d1ad69fbaa77358d2f78c5d2 + size: 214072 + - 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: 1bc51d09e02a975e4f02c956eb276f59 + size: 48 + - 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: 31e8b78ab0cc3ec2d9914289fa18e10f + size: 388420000 + depl_ASEMD_2: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_2 + deps: + - path: nodes/depl/ASEMD_1/metrics_dict.csv + hash: md5 + md5: ae03c002d1ad69fbaa77358d2f78c5d2 + size: 214072 + - 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: 1bc51d09e02a975e4f02c956eb276f59 + size: 48 + - 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: 31e8b78ab0cc3ec2d9914289fa18e10f + size: 388420000 + - path: nodes/final/MLModel/apax_model + hash: md5 + md5: 7bb083beece72942c4e9f6f6d9ae05cf.dir + size: 42264512 + nfiles: 6 + - path: nodes/final/MLModel/log.csv + hash: md5 + md5: 334bf3dbef993e8e9e812800e9709dce + size: 354541 + - path: nodes/final/MLModel/metrics.json + hash: md5 + md5: b4469fcc555cdbfbe570d0aa4e40f14f + size: 389 + - path: nodes/final/MLModel/node-meta.json + hash: md5 + md5: 970951f390e6d7586cae686fdd9f6dda + size: 48 + - path: nodes/final/MLModel/train_atoms.extxyz + hash: md5 + md5: c73f7ed92deedd952c59845bde00a0b0 + size: 48855065 + - path: nodes/final/MLModel/val_atoms.extxyz + hash: md5 + md5: 9eda8d89a8543dc151afc20daa607205 + size: 3188610 + params: + params.yaml: + depl_ASEMD_2: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 500000 + use_momenta: false + wrap: false + depl_ASEMD_2+thermostat: + pfactor: 54.273 + pressure: 6.324e-07 + temperature: 300 + tetragonal_strain: true + time_step: 1.0 + ttime: 2.4557 + outs: + - path: nodes/depl/ASEMD_2/metrics_dict.csv + hash: md5 + md5: 836e9a5c5f3688bc4d7f2555bf9e677a + size: 2191379 + - path: nodes/depl/ASEMD_2/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD_2/node-meta.json + hash: md5 + md5: 177b96abf89f3ad9e6976529a0f4cb97 + size: 48 + - path: nodes/depl/ASEMD_2/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD_2/trajectory.h5 + hash: md5 + md5: 2e34804f2d63789fd3d4cb6c9e90ee0d + size: 3854787616 + depl_AnalyseDensity: + cmd: zntrack run ipsuite.nodes.AnalyseDensity --name depl_AnalyseDensity + deps: + - path: nodes/depl/ASEMD_2/metrics_dict.csv + hash: md5 + md5: 836e9a5c5f3688bc4d7f2555bf9e677a + size: 2191379 + - path: nodes/depl/ASEMD_2/model + hash: md5 + md5: 64586897446153f477c052dd0e2579ad.dir + size: 11 + nfiles: 1 + - path: nodes/depl/ASEMD_2/node-meta.json + hash: md5 + md5: 177b96abf89f3ad9e6976529a0f4cb97 + size: 48 + - path: nodes/depl/ASEMD_2/steps_before_stopping.json + hash: md5 + md5: 6bb61e3b7bce0931da574d19d1d82c88 + size: 2 + - path: nodes/depl/ASEMD_2/trajectory.h5 + hash: md5 + md5: 2e34804f2d63789fd3d4cb6c9e90ee0d + size: 3854787616 + params: + params.yaml: + depl_AnalyseDensity: + end: + start: 0 + window: 1000 + outs: + - path: nodes/depl/AnalyseDensity/density.json + hash: md5 + md5: f05c48f59c0aee277f5bc8ed3932c4c4 + size: 65 + - path: nodes/depl/AnalyseDensity/density.png + hash: md5 + md5: 98ef49af98ea9e2cc3b14d842e1eab7c + size: 50270 + - path: nodes/depl/AnalyseDensity/node-meta.json + hash: md5 + md5: 8cd30475e5d9fb93702bcb5c160a36d7 + size: 48 + - path: nodes/depl/AnalyseDensity/results.csv + hash: md5 + md5: 1784a523cf90d65e1d6e6a2bee822be9 + size: 1198480 diff --git a/dvc.yaml b/dvc.yaml index f89d065..9325c71 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -179,6 +179,11 @@ plots: x_label: epochs y: val_loss y_label: validation loss +- nodes/depl/AnalyseDensity/density.png: {} +- nodes/depl/ASEMD/metrics_dict.csv: {} +- nodes/depl/ASEMD_1/metrics_dict.csv: {} +- nodes/depl/ASEMD_2/metrics_dict.csv: {} +- nodes/depl/AnalyseDensity/results.csv: {} stages: ML0_ConfigurationSelection: cmd: zntrack run ipsuite.nodes.BatchKernelSelection --name ML0_ConfigurationSelection @@ -264,7 +269,7 @@ 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 +379,7 @@ 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 +592,7 @@ 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 +652,7 @@ 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 +815,7 @@ 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 +973,7 @@ 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 +1210,7 @@ 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 +1296,7 @@ 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 +1432,7 @@ 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 +1519,7 @@ 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 +1789,7 @@ 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 +1897,7 @@ 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 +2002,7 @@ 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 +2111,7 @@ 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 +2228,7 @@ 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 +2337,7 @@ 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 +2466,7 @@ 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 +2575,7 @@ 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 +2716,7 @@ 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 +2826,7 @@ 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 +2979,7 @@ 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 +3089,7 @@ 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 +3254,7 @@ 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 +3364,7 @@ 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 +3541,7 @@ 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 +3651,7 @@ 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 +3840,7 @@ 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 +3950,7 @@ 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 +4151,7 @@ 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 +4436,7 @@ 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 +4653,7 @@ 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 +4748,7 @@ 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 +4859,7 @@ 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: @@ -4898,6 +4903,172 @@ stages: - nodes/classical/PredictionMetrics/stress_deviatoric_df.csv - nodes/classical/PredictionMetrics/stress_df.csv - nodes/classical/PredictionMetrics/stress_hydrostatic_df.csv + depl_ASEGeoOpt: + cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt + deps: + - nodes/depl/Packmol_1/atoms.h5 + - nodes/depl/Packmol_1/node-meta.json + - nodes/depl/Packmol_1/packmol + - nodes/final/MLModel/apax_model + - nodes/final/MLModel/log.csv + - nodes/final/MLModel/metrics.json + - nodes/final/MLModel/node-meta.json + - nodes/final/MLModel/train_atoms.extxyz + - nodes/final/MLModel/val_atoms.extxyz + 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/depl/ASEGeoOpt/model_outs + - nodes/depl/ASEGeoOpt/node-meta.json + - nodes/depl/ASEGeoOpt/trajectory.h5 + - nodes/final/MLModel/apax_model + - nodes/final/MLModel/log.csv + - nodes/final/MLModel/metrics.json + - nodes/final/MLModel/node-meta.json + - nodes/final/MLModel/train_atoms.extxyz + - nodes/final/MLModel/val_atoms.extxyz + 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/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 + - nodes/final/MLModel/apax_model + - nodes/final/MLModel/log.csv + - nodes/final/MLModel/metrics.json + - nodes/final/MLModel/node-meta.json + - nodes/final/MLModel/train_atoms.extxyz + - nodes/final/MLModel/val_atoms.extxyz + 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_ASEMD_2: + cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_2 + deps: + - 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 + - nodes/final/MLModel/apax_model + - nodes/final/MLModel/log.csv + - nodes/final/MLModel/metrics.json + - nodes/final/MLModel/node-meta.json + - nodes/final/MLModel/train_atoms.extxyz + - nodes/final/MLModel/val_atoms.extxyz + metrics: + - nodes/depl/ASEMD_2/node-meta.json: + cache: false + - nodes/depl/ASEMD_2/steps_before_stopping.json: + cache: false + outs: + - nodes/depl/ASEMD_2/metrics_dict.csv + - nodes/depl/ASEMD_2/model + - nodes/depl/ASEMD_2/trajectory.h5 + params: + - depl_ASEMD_2 + - depl_ASEMD_2+thermostat + depl_AnalyseDensity: + cmd: zntrack run ipsuite.nodes.AnalyseDensity --name depl_AnalyseDensity + deps: + - nodes/depl/ASEMD_2/metrics_dict.csv + - nodes/depl/ASEMD_2/model + - nodes/depl/ASEMD_2/node-meta.json + - nodes/depl/ASEMD_2/steps_before_stopping.json + - nodes/depl/ASEMD_2/trajectory.h5 + metrics: + - nodes/depl/AnalyseDensity/density.json: + cache: false + - nodes/depl/AnalyseDensity/node-meta.json: + cache: false + outs: + - nodes/depl/AnalyseDensity/density.png + - nodes/depl/AnalyseDensity/results.csv + params: + - depl_AnalyseDensity + 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: @@ -4967,7 +5138,7 @@ 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 +5250,7 @@ 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 +5293,31 @@ 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 +5378,8 @@ 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..f8c7f38 100644 --- a/main.py +++ b/main.py @@ -524,16 +524,91 @@ prediction = ips.analysis.Prediction(data=test_data, model=model) metrics = ips.analysis.PredictionMetrics(data=prediction) -with project.group("final_ensemble") as final: - model = ips.models.Apax( - data=train_data, - validation_data=validation_data.atoms, - config="config/final_ensemble.yaml", +# with project.group("final_ensemble") as final: +# model = ips.models.Apax( +# data=train_data, +# validation_data=validation_data.atoms, +# config="config/final_ensemble.yaml", +# ) +# prediction = ips.analysis.Prediction(data=test_data, model=model) +# metrics = ips.analysis.PredictionMetrics(data=prediction) + +# prediction = ips.analysis.Prediction(data=train_data, model=model) +# metrics = ips.analysis.PredictionMetrics(data=prediction) + +ramp_density = ips.calculators.RescaleBoxModifier( + density=1300 +) +thermostat = ips.calculators.LangevinThermostat( + temperature=300, friction=0.01, time_step=0.5 +) + +barostat = ips.calculators.NPTThermostat( + time_step=1.0, + temperature=300, + pressure=6.324e-07, # 1.01325 * units.bar, + ttime=2.4557, # 25 * units.fs, + pfactor=54.273, # (75 * units.fs) ** 2, + tetragonal_strain=True, ) - prediction = ips.analysis.Prediction(data=test_data, model=model) - metrics = ips.analysis.PredictionMetrics(data=prediction) - prediction = ips.analysis.Prediction(data=train_data, model=model) - metrics = ips.analysis.PredictionMetrics(data=prediction) +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=[32], + density=900, + ) + + geo_opt = ips.calculators.ASEGeoOpt( + model=model, + 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, + modifier=[ramp_density], + thermostat=thermostat, + steps=10_000, + sampling_rate=10, + ) + + eq_md = ips.calculators.ASEMD( + data=density_md.atoms, + data_id=-1, + model=model, + thermostat=thermostat, + steps=50_000, + sampling_rate=10, + ) + + md = ips.calculators.ASEMD( + data=eq_md.atoms, + data_id=-1, + model=model, + thermostat=barostat, + steps=500_000, + sampling_rate=10, + ) + + ips.analysis.AnalyseDensity(data=md.atoms) -project.build(nodes=[final]) +project.build(nodes=[depl]) diff --git a/nodes/depl/ASEGeoOpt/.gitignore b/nodes/depl/ASEGeoOpt/.gitignore new file mode 100644 index 0000000..68427bb --- /dev/null +++ b/nodes/depl/ASEGeoOpt/.gitignore @@ -0,0 +1,2 @@ +/trajectory.h5 +/model_outs diff --git a/nodes/depl/ASEGeoOpt/node-meta.json b/nodes/depl/ASEGeoOpt/node-meta.json new file mode 100644 index 0000000..b9ad73a --- /dev/null +++ b/nodes/depl/ASEGeoOpt/node-meta.json @@ -0,0 +1 @@ +{"uuid": "4f3dc5cf-102e-43c1-970d-b37eaa546846"} \ No newline at end of file diff --git a/nodes/depl/ASEMD/.gitignore b/nodes/depl/ASEMD/.gitignore new file mode 100644 index 0000000..c8ee395 --- /dev/null +++ b/nodes/depl/ASEMD/.gitignore @@ -0,0 +1,3 @@ +/trajectory.h5 +/model +/metrics_dict.csv diff --git a/nodes/depl/ASEMD/node-meta.json b/nodes/depl/ASEMD/node-meta.json new file mode 100644 index 0000000..6c7fc31 --- /dev/null +++ b/nodes/depl/ASEMD/node-meta.json @@ -0,0 +1 @@ +{"uuid": "de31bf96-f238-403e-9ac3-aba70585c879"} \ 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..c226ddb --- /dev/null +++ b/nodes/depl/ASEMD_1/.gitignore @@ -0,0 +1,3 @@ +/metrics_dict.csv +/trajectory.h5 +/model diff --git a/nodes/depl/ASEMD_1/node-meta.json b/nodes/depl/ASEMD_1/node-meta.json new file mode 100644 index 0000000..11a7039 --- /dev/null +++ b/nodes/depl/ASEMD_1/node-meta.json @@ -0,0 +1 @@ +{"uuid": "89a655a9-3b8f-4528-a33a-131b8918da8c"} \ 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/ASEMD_2/.gitignore b/nodes/depl/ASEMD_2/.gitignore new file mode 100644 index 0000000..c226ddb --- /dev/null +++ b/nodes/depl/ASEMD_2/.gitignore @@ -0,0 +1,3 @@ +/metrics_dict.csv +/trajectory.h5 +/model diff --git a/nodes/depl/ASEMD_2/node-meta.json b/nodes/depl/ASEMD_2/node-meta.json new file mode 100644 index 0000000..a704c44 --- /dev/null +++ b/nodes/depl/ASEMD_2/node-meta.json @@ -0,0 +1 @@ +{"uuid": "a0e31386-96a5-48e1-bca7-53e2a03a2903"} \ No newline at end of file diff --git a/nodes/depl/ASEMD_2/steps_before_stopping.json b/nodes/depl/ASEMD_2/steps_before_stopping.json new file mode 100644 index 0000000..d7d17fc --- /dev/null +++ b/nodes/depl/ASEMD_2/steps_before_stopping.json @@ -0,0 +1 @@ +-1 \ No newline at end of file diff --git a/nodes/depl/AnalyseDensity/.gitignore b/nodes/depl/AnalyseDensity/.gitignore new file mode 100644 index 0000000..ee34ece --- /dev/null +++ b/nodes/depl/AnalyseDensity/.gitignore @@ -0,0 +1,2 @@ +/density.png +/results.csv diff --git a/nodes/depl/AnalyseDensity/density.json b/nodes/depl/AnalyseDensity/density.json new file mode 100644 index 0000000..4f3119f --- /dev/null +++ b/nodes/depl/AnalyseDensity/density.json @@ -0,0 +1,4 @@ +{ + "density": 990.6212892162544, + "std": 21.5008684827742 +} \ No newline at end of file diff --git a/nodes/depl/AnalyseDensity/node-meta.json b/nodes/depl/AnalyseDensity/node-meta.json new file mode 100644 index 0000000..859e77b --- /dev/null +++ b/nodes/depl/AnalyseDensity/node-meta.json @@ -0,0 +1 @@ +{"uuid": "4cc97479-4cae-4778-82a7-69cb35f136d4"} \ 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..a73262a --- /dev/null +++ b/nodes/depl/Packmol_1/node-meta.json @@ -0,0 +1 @@ +{"uuid": "35bc2203-e340-441b-9e86-706090421cc2"} \ No newline at end of file diff --git a/nodes/depl/SmilesToAtoms/.gitignore b/nodes/depl/SmilesToAtoms/.gitignore new file mode 100644 index 0000000..9e6c0ed --- /dev/null +++ b/nodes/depl/SmilesToAtoms/.gitignore @@ -0,0 +1,2 @@ +/atoms.h5 +/molecule.png 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/nodes/final/MLModel/metrics.json b/nodes/final/MLModel/metrics.json index 04eb169..5177020 100644 --- a/nodes/final/MLModel/metrics.json +++ b/nodes/final/MLModel/metrics.json @@ -1,12 +1,12 @@ { "epoch": 1999.0, - "epoch_time": 5.338197946548462, - "train_energy_mae": 0.4733034282225413, - "train_forces_mae": 0.0391758753060593, - "train_loss": 0.0453446740400006, - "train_stress_mae": 5.625155990327214, - "val_energy_mae": 0.2957713909863378, - "val_forces_mae": 0.0641675313492599, - "val_loss": 0.1776181037925414, - "val_stress_mae": 6.87385545650633 + "epoch_time": 6.4727864265441895, + "train_energy_mae": 0.4700789870485574, + "train_forces_mae": 0.0398814458373313, + "train_loss": 0.048907139177592, + "train_stress_mae": 6.248454720275942, + "val_energy_mae": 0.3054888708351791, + "val_forces_mae": 0.0628271131425102, + "val_loss": 0.170694573568018, + "val_stress_mae": 7.535877414764008 } \ No newline at end of file diff --git a/nodes/final/MLModel/node-meta.json b/nodes/final/MLModel/node-meta.json index bd75006..cadcb58 100644 --- a/nodes/final/MLModel/node-meta.json +++ b/nodes/final/MLModel/node-meta.json @@ -1 +1 @@ -{"uuid": "0c7717d9-146b-4ba3-8fc0-2cedeb5357f9"} \ No newline at end of file +{"uuid": "bd522a3a-87fa-46ea-8498-4859d73eb40d"} \ No newline at end of file diff --git a/nodes/final/Prediction/node-meta.json b/nodes/final/Prediction/node-meta.json index 6d93fe9..f36646e 100644 --- a/nodes/final/Prediction/node-meta.json +++ b/nodes/final/Prediction/node-meta.json @@ -1 +1 @@ -{"uuid": "57ab3878-0163-4bce-a17b-be6631552c16"} \ No newline at end of file +{"uuid": "ea1c0863-324c-4ced-a576-876bbc357026"} \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/deviat_stress.json b/nodes/final/PredictionMetrics/deviat_stress.json index a6fe11d..9fcfe0b 100644 --- a/nodes/final/PredictionMetrics/deviat_stress.json +++ b/nodes/final/PredictionMetrics/deviat_stress.json @@ -1,8 +1,8 @@ { - "rmse": 0.000163541270445585, - "mse": 2.674574713895597e-08, - "mae": 0.00012959425434584516, - "max": 0.0006141899418202019, - "lp4": 3.945022897644709e-07, - "rrmse": 0.04488923713859736 + "rmse": 0.00015922776637606982, + "mse": 2.535348158511227e-08, + "mae": 0.0001267101179208166, + "max": 0.0005926276472868128, + "lp4": 3.822438356505371e-07, + "rrmse": 0.04370525522047232 } \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/energy.json b/nodes/final/PredictionMetrics/energy.json index 24dafde..7ead55e 100644 --- a/nodes/final/PredictionMetrics/energy.json +++ b/nodes/final/PredictionMetrics/energy.json @@ -1,8 +1,8 @@ { - "rmse": 1.6977488248369357, - "mse": 2.882351072235196, - "mae": 1.636038362487743, - "max": 2.869718057307182, - "lp4": 0.017043732873253285, - "rrmse": 0.5324658128432987 + "rmse": 1.9088408812195683, + "mse": 3.6436735098150983, + "mae": 1.8633169007622636, + "max": 2.96963313469314, + "lp4": 0.018818228872306456, + "rrmse": 0.5986707200369985 } \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/forces.json b/nodes/final/PredictionMetrics/forces.json index 279d30f..a4c7e85 100644 --- a/nodes/final/PredictionMetrics/forces.json +++ b/nodes/final/PredictionMetrics/forces.json @@ -1,8 +1,8 @@ { - "rmse": 89.79334635674645, - "mse": 8062.845049942632, - "mae": 51.48855935586135, - "max": 676.3785034548268, - "lp4": 0.021707630394808258, - "rrmse": 0.0762367270250828 + "rmse": 90.48625707544659, + "mse": 8187.762719523808, + "mae": 51.54513505373164, + "max": 663.8187273092167, + "lp4": 0.02200550496570018, + "rrmse": 0.07682502501661129 } \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/hydro_stress.json b/nodes/final/PredictionMetrics/hydro_stress.json index c46b2ec..4770daf 100644 --- a/nodes/final/PredictionMetrics/hydro_stress.json +++ b/nodes/final/PredictionMetrics/hydro_stress.json @@ -1,8 +1,8 @@ { - "rmse": 0.0006782252445744023, - "mse": 4.599894823780078e-07, - "mae": 0.0006611962512852509, - "max": 0.001103576305548911, - "lp4": 6.696834803079975e-06, - "rrmse": 0.20080017329431252 + "rmse": 0.0010377324770662912, + "mse": 1.0768886939581406e-06, + "mae": 0.001025445964497563, + "max": 0.0015468614445603296, + "lp4": 1.0038584110572994e-05, + "rrmse": 0.30723843279942703 } \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/node-meta.json b/nodes/final/PredictionMetrics/node-meta.json index 2fdc76c..16eb81d 100644 --- a/nodes/final/PredictionMetrics/node-meta.json +++ b/nodes/final/PredictionMetrics/node-meta.json @@ -1 +1 @@ -{"uuid": "80c2f660-71ef-4706-8fdd-f6bb10456a4a"} \ No newline at end of file +{"uuid": "21b64ee2-66e9-4653-9a73-6d62f56dd730"} \ No newline at end of file diff --git a/nodes/final/PredictionMetrics/stress.json b/nodes/final/PredictionMetrics/stress.json index 8341ec9..776d602 100644 --- a/nodes/final/PredictionMetrics/stress.json +++ b/nodes/final/PredictionMetrics/stress.json @@ -1,8 +1,8 @@ { - "rmse": 0.00042435312488338286, - "mse": 1.8007557459829192e-07, - "mae": 0.00030363623698439286, - "max": 0.001351565259034796, - "lp4": 1.057069246714105e-06, - "rrmse": 0.05781215391715819 + "rmse": 0.0006199325605024785, + "mse": 3.843163795711592e-07, + "mae": 0.0004247160705277836, + "max": 0.0018001557304079957, + "lp4": 1.5197299472015294e-06, + "rrmse": 0.08445710542576167 } \ No newline at end of file diff --git a/params.yaml b/params.yaml index e5d108b..973086f 100644 --- a/params.yaml +++ b/params.yaml @@ -951,6 +951,105 @@ classical_MLModel: 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: 1300 +depl_ASEMD+thermostat: + friction: 0.01 + temperature: 300 + 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: 50000 + use_momenta: false + wrap: false +depl_ASEMD_1+thermostat: + friction: 0.01 + temperature: 300 + time_step: 0.5 +depl_ASEMD_2: + data_id: -1 + dump_rate: 1000 + pop_last: false + repeat: + - 1 + - 1 + - 1 + sampling_rate: 10 + seed: 42 + steps: 500000 + use_momenta: false + wrap: false +depl_ASEMD_2+thermostat: + pfactor: 54.273 + pressure: 6.324e-07 + temperature: 300 + tetragonal_strain: true + time_step: 1.0 + ttime: 2.4557 +depl_AnalyseDensity: + end: null + start: 0 + window: 1000 +depl_Packmol: + box: null + count: + - 1 + - 1 + data_ids: null + density: 1210 + pbc: false + tolerance: 2.0 +depl_Packmol_1: + box: null + count: + - 32 + 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 c7e056c..8b65aff 100644 --- a/zntrack.json +++ b/zntrack.json @@ -16237,5 +16237,398 @@ "_type": "pathlib.Path", "value": "nodes/final_ensemble/PredictionMetrics_1" } + }, + "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, + "data": { + "_type": "znflow.Connection", + "value": { + "instance": { + "_type": "zntrack.Node", + "value": { + "module": 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