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schema: '2.0'
stages:
classical_AddData:
cmd: zntrack run ipsuite.nodes.AddData --name classical_AddData
deps:
- path: data/nvt_eq.xyz
hash: md5
md5: 38a194ced93c33e023a9eca895cf9d3b
size: 32692338
params:
params.yaml:
classical_AddData:
lines_to_read:
outs:
- path: nodes/classical/AddData/atoms.h5
hash: md5
md5: 4b28c7c0a6ae386fce15e8c814259378
size: 19874075
- path: nodes/classical/AddData/node-meta.json
hash: md5
md5: e875cc934db72ea4d2b9d3be558e88d1
size: 48
classical_ConfigurationSelection:
cmd: zntrack run ipsuite.nodes.RandomSelection --name classical_ConfigurationSelection
deps:
- path: nodes/classical/FilterOutlier/filtered_indices.json
hash: md5
md5: ca15d82dd94cdebcd4f2ee7229a1fc81
size: 28
- path: nodes/classical/FilterOutlier/histogram.png
hash: md5
md5: 9af8e55abe654af2487b7c2905c7def4
size: 26534
- path: nodes/classical/FilterOutlier/node-meta.json
hash: md5
md5: 218fd50cf426a933b2ed360ac97a315c
size: 48
params:
params.yaml:
classical_ConfigurationSelection:
n_configurations: 500
seed: 1234
outs:
- path: nodes/classical/ConfigurationSelection/node-meta.json
hash: md5
md5: f36b219c74c9d91264436d43a2205fcf
size: 48
- path: nodes/classical/ConfigurationSelection/selected_configurations.json
hash: md5
md5: 16197186b92aa023fd00cc3ac5f38582
size: 6763
- path: nodes/classical/ConfigurationSelection/selection.png
hash: md5
md5: af3a478f4fd3c8624841f79c50568cfe
size: 44259
classical_CP2KSinglePoint:
cmd: zntrack run ipsuite.nodes.CP2KSinglePoint --name classical_CP2KSinglePoint
deps:
- path: GTH_BASIS_SETS
hash: md5
md5: 518e733a7344699cf0b4192bb97eb6a3
size: 119403
- path: GTH_POTENTIALS
hash: md5
md5: 3a35b03b26b8ba5cf6c1d849dba11f15
size: 128982
- path: dftd3.dat
hash: md5
md5: 88745bcc951a4bcdccc4d6bcfa78d105
size: 1959318
- path: nodes/classical/AddData/atoms.h5
hash: md5
md5: 4b28c7c0a6ae386fce15e8c814259378
size: 19874075
- path: nodes/classical/AddData/node-meta.json
hash: md5
md5: e875cc934db72ea4d2b9d3be558e88d1
size: 48
params:
config/cp2k.yaml:
force_eval:
method: quickstep
DFT:
mgrid:
cutoff: 800
rel_cutoff: 60
ngrids: 5
QS:
eps_filter_matrix: 0.0
eps_pgf_orb: 0.0001
SCF:
scf_guess: restart
max_scf: 100
eps_scf: 1e-06
OT:
minimizer: diis
preconditioner: full_single_inverse
outer_scf:
max_scf: 100
eps_scf: 1e-06
print:
restart:
each:
QS_SCF: 0
XC:
xc_functional:
becke97:
parametrization: B97-3c
scale_c: 1.0
scale_x: 1.0
vdw_potential:
pair_potential:
type: dftd3(bj)
parameter_file_name: dftd3.dat
reference_functional: B97-3c
r_cutoff: 7.93766
calculate_c9_term: true
short_range_correction: true
potential_type: pair_potential
charge: 0
basis_set_file_name: GTH_BASIS_SETS
potential_file_name: GTH_POTENTIALS
subsys:
kind:
N:
basis_set: TZVP-GTH-q5
potential: GTH-PBE-q5
C:
basis_set: TZVP-GTH-q4
potential: GTH-PBE-q4
H:
basis_set: TZVP-GTH-q1
potential: GTH-PBE-q1
B:
basis_set: TZVP-GTH-q3
potential: GTH-PBE-q3
F:
basis_set: TZVP-GTH-q7
potential: GTH-PBE-q7
outs:
- path: nodes/classical/CP2KSinglePoint/atoms.h5
hash: md5
md5: 5517ee8f3037feee90b76352280cc493
size: 34653576
- path: nodes/classical/CP2KSinglePoint/cp2k
hash: md5
md5: 55489bae96a408ea6302c59d719d3ed0.dir
size: 138230425
nfiles: 3
- path: nodes/classical/CP2KSinglePoint/node-meta.json
hash: md5
md5: 54f69e1283b47e06e239ee0dc1deb23e
size: 48
final_MLModel:
cmd: zntrack run ipsuite.nodes.Apax --name final_MLModel
deps:
- path: nodes/ML0/ConfigurationSelection/node-meta.json
hash: md5
md5: c63ec9a3ee741eda364299fba9d1f33c
size: 48
- path: nodes/ML0/ConfigurationSelection/selected_configurations.json
hash: md5
md5: 2fe1ff3445c4d109b873252ee738fb21
size: 5298
- path: nodes/ML0/ConfigurationSelection/selection.png
hash: md5
md5: e69b22105f551142c8c5f216f6195135
size: 67448
- path: nodes/ML1/CP2KSinglePoint/atoms.h5
hash: md5
md5: 1a7a68f83340406aa1164f42bae049eb
size: 1252296
- path: nodes/ML1/CP2KSinglePoint/cp2k
hash: md5
md5: 85b8556d44d8ef6eea20d5ed509dd3ad.dir
size: 15159470
nfiles: 3
- path: nodes/ML1/CP2KSinglePoint/node-meta.json
hash: md5
md5: a874fce5c1681ffb680d7bee5dfccf97
size: 48
- path: nodes/ML10/CP2KSinglePoint/atoms.h5
hash: md5
md5: cc04f8c6d047a5cb46fcf5e8b4c5dc8e
size: 1252296
- path: nodes/ML10/CP2KSinglePoint/cp2k
hash: md5
md5: 0be17c2c2559a4981cd2ea7cf21ed123.dir
size: 15691448
nfiles: 3
- path: nodes/ML10/CP2KSinglePoint/node-meta.json
hash: md5
md5: abb5bfd72fb523275af2b02374a3744e
size: 48
- path: nodes/ML11_MultiPack/CP2KSinglePoint/atoms.h5
hash: md5
md5: 4acf2a8e643244dbe723a5f8c7689798
size: 379232
- path: nodes/ML11_MultiPack/CP2KSinglePoint/cp2k
hash: md5
md5: 8a2da0d10b09ea5d5eb00d568ae6fe44.dir
size: 13588720
nfiles: 3
- path: nodes/ML11_MultiPack/CP2KSinglePoint/node-meta.json
hash: md5
md5: 56022e78bbb05c34a46f9b442fc54aa9
size: 48
- path: nodes/ML12/CP2KSinglePoint/atoms.h5
hash: md5
md5: cae93a84f17fa4bcacaed525f61c445a
size: 1252296
- path: nodes/ML12/CP2KSinglePoint/cp2k
hash: md5
md5: abd9e5d874493b831c1d6377b348ecd6.dir
size: 15728011
nfiles: 3
- path: nodes/ML12/CP2KSinglePoint/node-meta.json
hash: md5
md5: 89c2a27e29a3645867b3608167bf5c90
size: 48
- path: nodes/ML13/CP2KSinglePoint/atoms.h5
hash: md5
md5: e6a997358a461fa9c1a360089fe33439
size: 1252296
- path: nodes/ML13/CP2KSinglePoint/cp2k
hash: md5
md5: 1c42e9152905e95c8d87fe697bf7b7c3.dir
size: 15916480
nfiles: 3
- path: nodes/ML13/CP2KSinglePoint/node-meta.json
hash: md5
md5: 20b1193a37c56a61921781b8a1dac857
size: 48
- path: nodes/ML14/CP2KSinglePoint/atoms.h5
hash: md5
md5: 7dc6e618240127f03242972b521d5768
size: 1252296
- path: nodes/ML14/CP2KSinglePoint/cp2k
hash: md5
md5: ff9f9cb9424dff857fa6db45e27be606.dir
size: 15957424
nfiles: 3
- path: nodes/ML14/CP2KSinglePoint/node-meta.json
hash: md5
md5: 523713af9dfc115d5e3da0f72f9922d7
size: 48
- path: nodes/ML15/CP2KSinglePoint/atoms.h5
hash: md5
md5: 9661310f5df5b53bcee014bd328113f7
size: 2504944
- path: nodes/ML15/CP2KSinglePoint/cp2k
hash: md5
md5: db033989bd1f9f7449179c6b93339fe4.dir
size: 19632655
nfiles: 3
- path: nodes/ML15/CP2KSinglePoint/node-meta.json
hash: md5
md5: 3d553e846c6ec3f4701a086439628aa5
size: 48
- path: nodes/ML2/CP2KSinglePoint/atoms.h5
hash: md5
md5: 7815747b6ed20c4c40ac55f96582c905
size: 1252296
- path: nodes/ML2/CP2KSinglePoint/cp2k
hash: md5
md5: a2fa20de295ec81ef85ca747acf80cef.dir
size: 15040654
nfiles: 3
- path: nodes/ML2/CP2KSinglePoint/node-meta.json
hash: md5
md5: 943e3651080de64d3f8748845f22d90c
size: 48
- path: nodes/ML3/CP2KSinglePoint/atoms.h5
hash: md5
md5: 472469d827b217f516d213d1c8192c48
size: 1252296
- path: nodes/ML3/CP2KSinglePoint/cp2k
hash: md5
md5: 3d64d0775e0af7dc2fa2ba0a643e282d.dir
size: 15157532
nfiles: 3
- path: nodes/ML3/CP2KSinglePoint/node-meta.json
hash: md5
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size: 48
- path: nodes/ML4/CP2KSinglePoint/atoms.h5
hash: md5
md5: 3a96da47e636a768335927069d3bb2c9
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- path: nodes/ML4/CP2KSinglePoint/cp2k
hash: md5
md5: 75c1c61f3f294f7db6a04a3979e73002.dir
size: 15155125
nfiles: 3
- path: nodes/ML4/CP2KSinglePoint/node-meta.json
hash: md5
md5: 29bfef9d2ff8d00dac6354848914ab56
size: 48
- path: nodes/ML5/CP2KSinglePoint/atoms.h5
hash: md5
md5: 0cffdeb327580b9f09bd993b10797bbe
size: 1252296
- path: nodes/ML5/CP2KSinglePoint/cp2k
hash: md5
md5: ab4116cfea96fbe3fa79f717d468123f.dir
size: 15161772
nfiles: 3
- path: nodes/ML5/CP2KSinglePoint/node-meta.json
hash: md5
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- path: nodes/ML6/CP2KSinglePoint/atoms.h5
hash: md5
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- path: nodes/ML6/CP2KSinglePoint/node-meta.json
hash: md5
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size: 48
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hash: md5
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hash: md5
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size: 15187689
nfiles: 3
- path: nodes/ML7/CP2KSinglePoint/node-meta.json
hash: md5
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- path: nodes/ML8/CP2KSinglePoint/atoms.h5
hash: md5
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hash: md5
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size: 15614026
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- path: nodes/ML8/CP2KSinglePoint/node-meta.json
hash: md5
md5: 4bb36a404075377f06bbfdf0a1fdf192
size: 48
- path: nodes/ML9/CP2KSinglePoint/atoms.h5
hash: md5
md5: 13742b3182554275e5bb17bb6d1d2f2e
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- path: nodes/ML9/CP2KSinglePoint/cp2k
hash: md5
md5: 4a5940fef000e02305243caadc1fb621.dir
size: 15671796
nfiles: 3
- path: nodes/ML9/CP2KSinglePoint/node-meta.json
hash: md5
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size: 48
- path: nodes/VS/CP2KSinglePoint/atoms.h5
hash: md5
md5: 1a495c0e3bd86f6bed1d35c8cb51f18e
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- path: nodes/VS/CP2KSinglePoint/cp2k
hash: md5
md5: df6785e31717cef9ae2d50f24e93ddac.dir
size: 15867639
nfiles: 3
- path: nodes/VS/CP2KSinglePoint/node-meta.json
hash: md5
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size: 48
- path: nodes/classical/ConfigurationSelection_1/node-meta.json
hash: md5
md5: 214a8afd08f14201c2d2d7a5004d646e
size: 48
- path: nodes/classical/ConfigurationSelection_1/selected_configurations.json
hash: md5
md5: b574b1f0ff57372a517d7eeb93ace532
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- path: nodes/classical/ConfigurationSelection_1/selection.png
hash: md5
md5: 740759b3fb81dc973f8979ae133161f9
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- path: nodes/classical/ConfigurationSelection_2/node-meta.json
hash: md5
md5: c96f98e7ac534af9e7177c90e44ba98c
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- path: nodes/classical/ConfigurationSelection_2/selected_configurations.json
hash: md5
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size: 1381
- path: nodes/classical/ConfigurationSelection_2/selection.png
hash: md5
md5: 8afeba13916f368f55bd5c2626f11a65
size: 43456
params:
params.yaml:
final_MLModel:
jax_enable_x64: true
use_energy: true
use_forces: true
use_stresses: false
config/final.yaml:
data:
batch_size: 8
scale_method: per_element_force_rms_scale
shift_method: per_element_regression_shift
shift_options:
energy_regularisation: 1.0
valid_batch_size: 100
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: 5.5
r_min: 0.7
b_init: zeros
emb_init: uniform
calc_stress: true
use_zbl: true
descriptor_dtype: fp32
readout_dtype: fp32
scale_shift_dtype: fp32
n_epochs: 2000
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
seed: 1
outs:
- path: nodes/final/MLModel/apax_model
hash: md5
md5: 43a89a7107bfa23dd83e472d5636dac2.dir
size: 42264512
nfiles: 6
- path: nodes/final/MLModel/log.csv
hash: md5
md5: e9c76ff0a77b1ee26f58292bbd138e38
size: 354570
- path: nodes/final/MLModel/metrics.json
hash: md5
md5: b7e8ff6bf0986a7ebb6785a3e0e03efa
size: 389
- path: nodes/final/MLModel/node-meta.json
hash: md5
md5: 94d46c83d6bc474f48dd5eaecc2e5db6
size: 48
- path: nodes/final/MLModel/train_atoms.extxyz
hash: md5
md5: 6e7cf112aa5205bac393bedc3e3152a5
size: 53574955
- path: nodes/final/MLModel/val_atoms.extxyz
hash: md5
md5: 9eda8d89a8543dc151afc20daa607205
size: 3188610
final_Prediction:
cmd: zntrack run ipsuite.nodes.Prediction --name final_Prediction
deps:
- path: nodes/classical/ConfigurationSelection/node-meta.json
hash: md5
md5: f36b219c74c9d91264436d43a2205fcf
size: 48
- path: nodes/classical/ConfigurationSelection/selected_configurations.json
hash: md5
md5: 16197186b92aa023fd00cc3ac5f38582
size: 6763
- path: nodes/classical/ConfigurationSelection/selection.png
hash: md5
md5: af3a478f4fd3c8624841f79c50568cfe
size: 44259
- path: nodes/final/MLModel/apax_model
hash: md5
md5: 43a89a7107bfa23dd83e472d5636dac2.dir
size: 42264512
nfiles: 6
- path: nodes/final/MLModel/log.csv
hash: md5
md5: e9c76ff0a77b1ee26f58292bbd138e38
size: 354570
- path: nodes/final/MLModel/metrics.json
hash: md5
md5: b7e8ff6bf0986a7ebb6785a3e0e03efa
size: 389
- path: nodes/final/MLModel/node-meta.json
hash: md5
md5: 94d46c83d6bc474f48dd5eaecc2e5db6
size: 48
- path: nodes/final/MLModel/train_atoms.extxyz
hash: md5
md5: 6e7cf112aa5205bac393bedc3e3152a5
size: 53574955
- path: nodes/final/MLModel/val_atoms.extxyz
hash: md5
md5: 9eda8d89a8543dc151afc20daa607205
size: 3188610
outs:
- path: nodes/final/Prediction/atoms.h5
hash: md5
md5: 44dff8a819bbfcf3cad635d72e55badf
size: 8722872
- path: nodes/final/Prediction/node-meta.json
hash: md5
md5: 8a5ac6aaab1a96c95f5bbf05d81ee4ad
size: 48
final_PredictionMetrics:
cmd: zntrack run ipsuite.nodes.PredictionMetrics --name final_PredictionMetrics
deps:
- path: nodes/final/Prediction/atoms.h5
hash: md5
md5: 44dff8a819bbfcf3cad635d72e55badf
size: 8722872
- path: nodes/final/Prediction/node-meta.json
hash: md5
md5: 8a5ac6aaab1a96c95f5bbf05d81ee4ad
size: 48
outs:
- path: nodes/final/PredictionMetrics/deviat_stress.json
hash: md5
md5: 1bc64419ffabe8a20144d7c83374177f
size: 208
- path: nodes/final/PredictionMetrics/energy.json
hash: md5
md5: e5b50e5eaaac5b5221fdba05b7a89e6a
size: 187
- path: nodes/final/PredictionMetrics/energy_df.csv
hash: md5
md5: 83099995a1102b7b0366586847b2713b
size: 21333
- path: nodes/final/PredictionMetrics/forces.json
hash: md5
md5: 525327c775880b80191b26e42ef39a92
size: 189
- path: nodes/final/PredictionMetrics/forces_df.csv
hash: md5
md5: f6b270cc13ac3d97a65148eadbf3e05a
size: 22661484
- path: nodes/final/PredictionMetrics/hydro_stress.json
hash: md5
md5: df0b621926cf5384a2377959784777ed
size: 205
- path: nodes/final/PredictionMetrics/node-meta.json
hash: md5
md5: cdb8c99d4140dfb345e585afbdac9d5e
size: 48
- path: nodes/final/PredictionMetrics/plots
hash: md5
md5: 878df8a528f690663ac7da3e61afdc06.dir
size: 360036
nfiles: 5
- path: nodes/final/PredictionMetrics/stress.json
hash: md5
md5: 1a529757c092c3add3801e505dadd5d8
size: 209
- path: nodes/final/PredictionMetrics/stress_deviatoric_df.csv
hash: md5
md5: f5089acf9331bd287b9eec023c9c0ede
size: 212046
- path: nodes/final/PredictionMetrics/stress_df.csv
hash: md5
md5: 6172fabe2d028ddd38d71169b5d92d9f
size: 207531
- path: nodes/final/PredictionMetrics/stress_hydrostatic_df.csv
hash: md5
md5: c24ece25d3db8538df67e64552624156
size: 23521
md_SmilesToAtoms:
cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name md_SmilesToAtoms
params:
params.yaml:
md_SmilesToAtoms:
cell:
optimizer: UFF
seed: 1234
smiles: CCCCN1C=C[N+](=C1)C
outs:
- path: nodes/md/SmilesToAtoms/atoms.h5
hash: md5
md5: 744f94e60270ed284980820ff3038f19
size: 27968
- path: nodes/md/SmilesToAtoms/molecule.png
hash: md5
md5: 4a1d55d11840e8044a618e690876c465
size: 7734
- path: nodes/md/SmilesToAtoms/node-meta.json
hash: md5
md5: 035e3cc28e26d5acd440419e9d72e785
size: 48
md_SmilesToAtoms_1:
cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name md_SmilesToAtoms_1
params:
params.yaml:
md_SmilesToAtoms_1:
cell:
optimizer: UFF
seed: 1234
smiles: '[B-](F)(F)(F)F'
outs:
- path: nodes/md/SmilesToAtoms_1/atoms.h5
hash: md5
md5: 181a42114d5c08d6ac24e8ce30a8f82b
size: 27968
- path: nodes/md/SmilesToAtoms_1/molecule.png
hash: md5
md5: 2f3c76af0d99ecffdf812f2e6341aa50
size: 2963
- path: nodes/md/SmilesToAtoms_1/node-meta.json
hash: md5
md5: d76fe4aeb8451367b3aa3fa21d909e85
size: 48
md_Packmol:
cmd: zntrack run ipsuite.nodes.Packmol --name md_Packmol
deps:
- path: nodes/md/SmilesToAtoms/atoms.h5
hash: md5
md5: 744f94e60270ed284980820ff3038f19
size: 27968
- path: nodes/md/SmilesToAtoms/molecule.png
hash: md5
md5: 4a1d55d11840e8044a618e690876c465
size: 7734
- path: nodes/md/SmilesToAtoms/node-meta.json
hash: md5
md5: 035e3cc28e26d5acd440419e9d72e785
size: 48
- path: nodes/md/SmilesToAtoms_1/atoms.h5
hash: md5
md5: 181a42114d5c08d6ac24e8ce30a8f82b
size: 27968
- path: nodes/md/SmilesToAtoms_1/molecule.png
hash: md5
md5: 2f3c76af0d99ecffdf812f2e6341aa50
size: 2963
- path: nodes/md/SmilesToAtoms_1/node-meta.json
hash: md5
md5: d76fe4aeb8451367b3aa3fa21d909e85
size: 48
params:
params.yaml:
md_Packmol:
box:
count:
- 1
- 1
data_ids:
density: 1210
tolerance: 2.0
outs:
- path: nodes/md/Packmol/atoms.h5
hash: md5
md5: c32f2190bc1f40d5bb4587a7b4741bea
size: 27968
- path: nodes/md/Packmol/node-meta.json
hash: md5
md5: 793c3a55e9cfdfa5e4ad893ab616c18d
size: 48
- path: nodes/md/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
size: 3841
nfiles: 4
md_Packmol_1:
cmd: zntrack run ipsuite.nodes.Packmol --name md_Packmol_1
deps:
- path: nodes/md/Packmol/atoms.h5
hash: md5
md5: c32f2190bc1f40d5bb4587a7b4741bea
size: 27968
- path: nodes/md/Packmol/node-meta.json
hash: md5
md5: 793c3a55e9cfdfa5e4ad893ab616c18d
size: 48
- path: nodes/md/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
size: 3841
nfiles: 4
params:
params.yaml:
md_Packmol_1:
box:
count:
- 100
data_ids:
density: 1210
tolerance: 2.0
outs:
- path: nodes/md/Packmol_1/atoms.h5
hash: md5
md5: a47814b6d895ea2f1207901bdf707559
size: 147968
- path: nodes/md/Packmol_1/node-meta.json
hash: md5
md5: 1e8c82d828a742a0cf292aa1ef4c0d41
size: 48
- path: nodes/md/Packmol_1/packmol
hash: md5
md5: afacb6f9c8d766db6fd2c5a7d6b7fba7.dir
size: 170063
nfiles: 3
SmilesToAtoms:
cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name SmilesToAtoms
params:
params.yaml:
SmilesToAtoms:
cell:
optimizer: UFF
seed: 1234
smiles: CCCCN1C=C[N+](=C1)C
outs:
- path: nodes/SmilesToAtoms/atoms.h5
hash: md5
md5: 744f94e60270ed284980820ff3038f19
size: 27968
- path: nodes/SmilesToAtoms/molecule.png
hash: md5
md5: 4a1d55d11840e8044a618e690876c465
size: 7734
- path: nodes/SmilesToAtoms/node-meta.json
hash: md5
md5: 6a98e77188f2c120a3674b49ff0dfcaa
size: 48
SmilesToAtoms_1:
cmd: zntrack run ipsuite.nodes.SmilesToAtoms --name SmilesToAtoms_1
params:
params.yaml:
SmilesToAtoms_1:
cell:
optimizer: UFF
seed: 1234
smiles: '[B-](F)(F)(F)F'
outs:
- path: nodes/SmilesToAtoms_1/atoms.h5
hash: md5
md5: 181a42114d5c08d6ac24e8ce30a8f82b
size: 27968
- path: nodes/SmilesToAtoms_1/molecule.png
hash: md5
md5: 2f3c76af0d99ecffdf812f2e6341aa50
size: 2963
- path: nodes/SmilesToAtoms_1/node-meta.json
hash: md5
md5: 4abc4e85603cb34274af082be1b70aff
size: 48
Packmol:
cmd: zntrack run ipsuite.nodes.Packmol --name Packmol
deps:
- path: nodes/SmilesToAtoms/atoms.h5
hash: md5
md5: 744f94e60270ed284980820ff3038f19
size: 27968
- path: nodes/SmilesToAtoms/molecule.png
hash: md5
md5: 4a1d55d11840e8044a618e690876c465
size: 7734
- path: nodes/SmilesToAtoms/node-meta.json
hash: md5
md5: 6a98e77188f2c120a3674b49ff0dfcaa
size: 48
- path: nodes/SmilesToAtoms_1/atoms.h5
hash: md5
md5: 181a42114d5c08d6ac24e8ce30a8f82b
size: 27968
- path: nodes/SmilesToAtoms_1/molecule.png
hash: md5
md5: 2f3c76af0d99ecffdf812f2e6341aa50
size: 2963
- path: nodes/SmilesToAtoms_1/node-meta.json
hash: md5
md5: 4abc4e85603cb34274af082be1b70aff
size: 48
params:
params.yaml:
Packmol:
box:
count:
- 1
- 1
data_ids:
density: 1210
tolerance: 2.0
outs:
- path: nodes/Packmol/atoms.h5
hash: md5
md5: c32f2190bc1f40d5bb4587a7b4741bea
size: 27968
- path: nodes/Packmol/node-meta.json
hash: md5
md5: ca0aa6704f351ab3fb6d2c973721df73
size: 48
- path: nodes/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
size: 3841
nfiles: 4
Packmol_1:
cmd: zntrack run ipsuite.nodes.Packmol --name Packmol_1
deps:
- path: nodes/Packmol/atoms.h5
hash: md5
md5: c32f2190bc1f40d5bb4587a7b4741bea
size: 27968
- path: nodes/Packmol/node-meta.json
hash: md5
md5: ca0aa6704f351ab3fb6d2c973721df73
size: 48
- path: nodes/Packmol/packmol
hash: md5
md5: 9211f580932fa95a1d122b0e2be6699c.dir
size: 3841
nfiles: 4
params:
params.yaml:
Packmol_1:
box:
count:
- 10
data_ids:
density: 1210
tolerance: 2.0
outs:
- path: nodes/Packmol_1/atoms.h5
hash: md5
md5: 004fbeec002d78da2d14ecd32a86e97f
size: 37568
- path: nodes/Packmol_1/node-meta.json
hash: md5
md5: 001f51c65ee7e51acee1f533075894dc
size: 48
- path: nodes/Packmol_1/packmol
hash: md5
md5: 803319a22bc76fdaa5ee9e53cbf58e82.dir
size: 18862
nfiles: 3
ASEGeoOpt:
cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name ASEGeoOpt
deps:
- path: nodes/classical/AddData/atoms.h5
hash: md5
md5: 4b28c7c0a6ae386fce15e8c814259378
size: 19874075
- path: nodes/classical/AddData/node-meta.json
hash: md5
md5: e875cc934db72ea4d2b9d3be558e88d1
size: 48
- path: nodes/final/ApaxEnsemble/node-meta.json
hash: md5
md5: 2c156e4a3c7dcde93ed09da94be1dee8
size: 48
params:
params.yaml:
ASEGeoOpt:
data_id: 0
dump_rate: 1000
init_kwargs: {}
optimizer: FIRE
repeat:
- 1
- 1
- 1
run_kwargs:
fmax: 0.1
outs:
- path: nodes/ASEGeoOpt/model_outs
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/ASEGeoOpt/node-meta.json
hash: md5
md5: 657b944a0eef3dce37f4b2f5a8bc16dc
size: 48
- path: nodes/ASEGeoOpt/trajectory.h5
hash: md5
md5: 64c4845c1101d1bb701e8a498c31342a
size: 1432040
final_MLModel_1:
cmd: zntrack run ipsuite.nodes.Apax --name final_MLModel_1
deps:
- path: nodes/classical/ConfigurationSelection/node-meta.json
hash: md5
md5: 5b74c0c06b9ae3e1a5cc5369dadd5309
size: 48
- path: nodes/classical/ConfigurationSelection/selected_configurations.json
hash: md5
md5: afce37868d81f40b08ad4ba6c68222f5
size: 13485
- path: nodes/classical/ConfigurationSelection/selection.png
hash: md5
md5: bb69658e118dfa06a7aa1844fbb30105
size: 35869
params:
params.yaml:
final_MLModel_1:
jax_enable_x64: true
use_energy: true
use_forces: true
use_stresses: false
config/initial_model_2.yaml:
data:
batch_size: 8
scale_method: per_element_force_rms_scale
shift_method: per_element_regression_shift
shift_options:
energy_regularisation: 1.0
valid_batch_size: 100
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: 5.5
r_min: 0.7
b_init: zeros
emb_init: uniform
calc_stress: true
use_zbl: true
descriptor_dtype: fp32
readout_dtype: fp32
scale_shift_dtype: fp32
n_epochs: 2048
optimizer:
opt_name: adam
emb_lr: 0.01
nn_lr: 0.005
scale_lr: 0.001
shift_lr: 0.05
zbl_lr: 0.001
seed: 2
outs:
- path: nodes/final/MLModel_1/apax_model
hash: md5
md5: c2814a1e99e230d08348d0ffd0829e12.dir
size: 42263355
nfiles: 5
- path: nodes/final/MLModel_1/log.csv
hash: md5
md5: 109fc6ad835efa23bf88a56bdc4c643f
size: 363883
- path: nodes/final/MLModel_1/metrics.json
hash: md5
md5: 8e24e9bcf8989d2b6ce136d520e0463d
size: 390
- path: nodes/final/MLModel_1/node-meta.json
hash: md5
md5: 8db1f9228759568ef4bb467383f00138
size: 48
- path: nodes/final/MLModel_1/train.log
hash: md5
md5: 30b0a7c6fe3e4413f4a25a824acec52d
size: 19
- path: nodes/final/MLModel_1/train_atoms.extxyz
hash: md5
md5: c01eb40c254758e2acb945131018495c
size: 31885899
- path: nodes/final/MLModel_1/val_atoms.extxyz
hash: md5