Running without AiiDA

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import json
from xtalpaint.inpainting.config_schema import XtalPaintConfig
from xtalpaint.utils.relaxation_utils import relax_structures
from ase.io import read
from pymatgen.io.ase import AseAtomsAdaptor
from IPython.display import clear_output
import json
from xtalpaint.inpainting.config_schema import XtalPaintConfig
from xtalpaint.utils.relaxation_utils import relax_structures
from ase.io import read
from pymatgen.io.ase import AseAtomsAdaptor
from IPython.display import clear_output

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input_structures = read("test-structures.extxyz", index=':')
input_structures = {
    a.info['uuid'].replace("-", "_"): AseAtomsAdaptor.get_structure(a) for a in input_structures
}
input_structures = read("test-structures.extxyz", index=':')
input_structures = {
    a.info['uuid'].replace("-", "_"): AseAtomsAdaptor.get_structure(a) for a in input_structures
}

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len(input_structures)
len(input_structures)

Out[3]:

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param_grid = {
    "N_steps": 5,
    "coordinates_snr": 0.2,
    "n_corrector_steps": 1,
    "batch_size": 1000,
}
param_grid = {
    "N_steps": 5,
    "coordinates_snr": 0.2,
    "n_corrector_steps": 1,
    "batch_size": 1000,
}

Note on the model. This example uses our recommended TD-pos-only model — the core model of XtalPaint — with the time-dependent (TD) predictor-corrector. The XtalPaint models are downloaded automatically from Hugging Face the first time they are selected (you can also fetch one explicitly via xtalpaint.models.download_pretrained_model). See the configuration guide for the available model and predictor-corrector combinations.

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inputs = XtalPaintConfig(
    candidate_generation={
        "n_inp": {
            k.replace("-", "_"): int(s.composition["H"])
            for k, s in input_structures.items()
        },
        "element": "H",
        "num_samples": 1,
    },
    inpainting={
        "record_trajectories": False,
        "predictor_corrector": "TD",
        **param_grid,
        "pretrained_name": "TD-pos-only",
        "sampling_config_path": "../mattergen-configs/sampling_conf",
    },
    relaxation={
        "constrained": True,
        "full": True,
        "relax_config": {
            "params": {
                "mlip": "mattersim",
                "optimizer": "BFGS",
                "load_path": "MatterSim-v1.0.0-5M.pth",
                "fmax": 0.01,
                "max_n_steps": 50,
                "max_natoms_per_batch": 5000,
                "device": "cpu",
                "elements_to_relax": ["H"],
                "return_initial_energies": False,
                "return_initial_forces": False,
                "return_final_forces": False,
            },
            "aiida": None,
        },
    },
)
inputs = XtalPaintConfig(
    candidate_generation={
        "n_inp": {
            k.replace("-", "_"): int(s.composition["H"])
            for k, s in input_structures.items()
        },
        "element": "H",
        "num_samples": 1,
    },
    inpainting={
        "record_trajectories": False,
        "predictor_corrector": "TD",
        **param_grid,
        "pretrained_name": "TD-pos-only",
        "sampling_config_path": "../mattergen-configs/sampling_conf",
    },
    relaxation={
        "constrained": True,
        "full": True,
        "relax_config": {
            "params": {
                "mlip": "mattersim",
                "optimizer": "BFGS",
                "load_path": "MatterSim-v1.0.0-5M.pth",
                "fmax": 0.01,
                "max_n_steps": 50,
                "max_natoms_per_batch": 5000,
                "device": "cpu",
                "elements_to_relax": ["H"],
                "return_initial_energies": False,
                "return_initial_forces": False,
                "return_final_forces": False,
            },
            "aiida": None,
        },
    },
)

MODELS_PROJECT_ROOT: /home/reents_t/project/test-xtalpaint/mattergen-clean/mattergen

Running the inpainting workflow without AiiDA¶

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print(f"Processing {len(input_structures)} structures")
print(f"Processing {len(input_structures)} structures")

Processing 5 structures

Generate inpainting candidates¶

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from xtalpaint.inpainting.generate_candidates import (
    generate_inpainting_candidates,
)
from xtalpaint.inpainting.generate_candidates import (
    generate_inpainting_candidates,
)

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# Step 1: Generate inpainting candidates
print("Running inpainting pipeline...")

n_inp_dict = inputs.candidate_generation.n_inp
element = inputs.candidate_generation.element
num_samples = inputs.candidate_generation.num_samples

inpainting_candidates = generate_inpainting_candidates(
    structures=input_structures,
    n_inp=n_inp_dict,
    element=element,
    num_samples=num_samples,
)

print(f"Generated {len(inpainting_candidates)} inpainted structures")
# Step 1: Generate inpainting candidates
print("Running inpainting pipeline...")

n_inp_dict = inputs.candidate_generation.n_inp
element = inputs.candidate_generation.element
num_samples = inputs.candidate_generation.num_samples

inpainting_candidates = generate_inpainting_candidates(
    structures=input_structures,
    n_inp=n_inp_dict,
    element=element,
    num_samples=num_samples,
)

print(f"Generated {len(inpainting_candidates)} inpainted structures")

Running inpainting pipeline...
Generated 5 inpainted structures

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inpainting_candidates
inpainting_candidates

Out[9]:

{'20acc66e_8e38_4e5e_9e7a_c2400262cdc8': Structure Summary
 Lattice
     abc : 5.169783747 5.169783747 5.169783747
  angles : 90.0 90.0 90.0
  volume : 138.17107311088554
       A : 5.169783747 0.0 0.0
       B : 0.0 5.169783747 0.0
       C : 0.0 0.0 5.169783747
     pbc : True True True
 PeriodicSite: N (2.309, 4.894, 2.86) [0.4467, 0.9467, 0.5533]
 PeriodicSite: N (4.894, 2.86, 2.309) [0.9467, 0.5533, 0.4467]
 PeriodicSite: N (2.86, 2.309, 4.894) [0.5533, 0.4467, 0.9467]
 PeriodicSite: N (0.2756, 0.2756, 0.2756) [0.0533, 0.0533, 0.0533]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan],
 '47b9a869_9b1e_438b_8c93_f5ac654bfdd8': Structure Summary
 Lattice
     abc : 4.401448665821795 4.401448665821795 7.1759779644947
  angles : 90.0 90.0 120.19000916247398
  volume : 120.16231769034825
       A : 2.1944008576909 -3.8154102313683 0.0
       B : 2.1944008576909 3.8154102313683 0.0
       C : 0.0 0.0 7.1759779644947
     pbc : True True True
 PeriodicSite: O (2.194, 2.549, 3.886) [0.1659, 0.8341, 0.5415]
 PeriodicSite: O (7.744e-18, 1.266, 0.2978) [-0.1659, 0.1659, 0.0415]
 PeriodicSite: O (2.194, 2.544, 6.579) [0.1666, 0.8334, 0.9168]
 PeriodicSite: O (1.254e-17, 1.272, 2.991) [-0.1666, 0.1666, 0.4168]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan],
 '662c7351_ee76_48ea_bab7_b733e1fdf607': Structure Summary
 Lattice
     abc : 8.414296245395509 8.414296245395509 8.414296245395509
  angles : 93.51670444494472 93.51670444494472 151.3208570539183
  volume : 276.98877799736266
       A : -5.7644391936362 5.7644391936362 2.0839536633569
       B : 5.7644391936362 -5.7644391936362 2.0839536633569
       C : 5.7644391936362 5.7644391936362 -2.0839536633569
     pbc : True True True
 PeriodicSite: O (4.413e-16, 8.82, -0.1928) [0.7188, -0.04627, 0.7651]
 PeriodicSite: O (7.129e-17, 3.056, 1.235) [0.5613, 0.2963, 0.2651]
 PeriodicSite: O (7.664e-17, 2.709, -0.1928) [0.1887, -0.04627, 0.2349]
 PeriodicSite: O (7.102e-16, 8.473, 1.235) [1.031, 0.2963, 0.7349]
 PeriodicSite: O (3.056, 5.764, 2.277) [1.046, 0.8113, 0.7651]
 PeriodicSite: O (8.82, 5.764, 0.8491) [0.7037, 0.9688, 1.265]
 PeriodicSite: O (8.473, 5.764, 2.277) [1.046, 1.281, 1.235]
 PeriodicSite: O (2.709, 5.764, 0.8491) [0.7037, 0.4387, 0.7349]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan],
 '7fa282c5_4971_46f4_8b3b_776595a0fa06': Structure Summary
 Lattice
     abc : 6.3321144796 6.332114479595774 6.603633127
  angles : 90.0 90.0 120.00000000002208
  volume : 229.3037119499634
       A : 6.3321144796 0.0 0.0
       B : -3.1660572398 5.483771999 0.0
       C : 0.0 0.0 6.603633127
     pbc : True True True
 PeriodicSite: Y (2.099, 3.636, 1.651) [0.6631, 0.6631, 0.25]
 PeriodicSite: Y (4.199, 0.0, 4.953) [0.6631, 0.0, 0.75]
 PeriodicSite: Y (-2.099, 3.636, 4.953) [-6.806e-10, 0.6631, 0.75]
 PeriodicSite: Y (-1.067, 1.848, 1.651) [7.402e-10, 0.3369, 0.25]
 PeriodicSite: Y (1.067, 1.848, 4.953) [0.3369, 0.3369, 0.75]
 PeriodicSite: Y (2.134, 0.0, 1.651) [0.3369, 0.0, 0.25]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan],
 'c436bbf4_9aef_44a8_8960_00227f79a32f': Structure Summary
 Lattice
     abc : 4.9620535714985 5.689428317103 4.4034011624103
  angles : 90.0 90.0 90.0
  volume : 124.31351070276466
       A : 4.9620535714985 0.0 0.0
       B : 0.0 5.689428317103 0.0
       C : 0.0 0.0 4.4034011624103
     pbc : True True True
 PeriodicSite: V (2.481, 1.451, 2.02) [0.5, 0.2551, 0.4587]
 PeriodicSite: V (-2.13e-06, 4.238, 2.02) [-4.293e-07, 0.7449, 0.4587]
 PeriodicSite: V (2.481, 4.238, 2.02) [0.5, 0.7449, 0.4587]
 PeriodicSite: V (2.13e-06, 1.451, 2.02) [4.293e-07, 0.2551, 0.4587]
 PeriodicSite: V (2.481, 2.845, -0.1521) [0.5, 0.5, -0.03455]
 PeriodicSite: V (0.0, 2.845, -0.1521) [0.0, 0.5, -0.03455]
 PeriodicSite: V (2.481, 0.0, -0.1605) [0.5, 0.0, -0.03644]
 PeriodicSite: V (0.0, 0.0, -0.1605) [0.0, 0.0, -0.03644]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]
 PeriodicSite: H (nan, nan, nan) [nan, nan, nan]}

Run inpainting¶

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from xtalpaint.inpainting.inpainting_process import (
    run_inpainting_pipeline,
    run_mpi_parallel_inpainting_pipeline,
)
from xtalpaint.inpainting.inpainting_process import (
    run_inpainting_pipeline,
    run_mpi_parallel_inpainting_pipeline,
)

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USE_MPI_FOR_PARALLEL_INPAINTING = False

inpainting_method = (
    run_mpi_parallel_inpainting_pipeline
    if USE_MPI_FOR_PARALLEL_INPAINTING
    else run_inpainting_pipeline
)
USE_MPI_FOR_PARALLEL_INPAINTING = False

inpainting_method = (
    run_mpi_parallel_inpainting_pipeline
    if USE_MPI_FOR_PARALLEL_INPAINTING
    else run_inpainting_pipeline
)

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config = inputs.inpainting.model_dump(exclude_none=True)

inpainting_outputs = run_inpainting_pipeline(
    structures=inpainting_candidates, config=config
)

clear_output()
config = inputs.inpainting.model_dump(exclude_none=True)

inpainting_outputs = run_inpainting_pipeline(
    structures=inpainting_candidates, config=config
)

clear_output()

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inpainting_outputs['structures'].get_structures(strct_type='pymatgen')
inpainting_outputs['structures'].get_structures(strct_type='pymatgen')

Out[13]:

{'20acc66e_8e38_4e5e_9e7a_c2400262cdc8': Structure Summary
 Lattice
     abc : 5.1697835922241255 5.1697835922241255 5.169783592224121
  angles : 90.00000250447799 90.00000250447799 90.00000250447816
  volume : 138.171060700957
       A : 5.169783592224121 0.0 -2.2597841109472938e-07
       B : -2.2597843664143413e-07 5.169783592224116 -2.2597841109472938e-07
       C : 0.0 0.0 5.169783592224121
     pbc : True True True
 PeriodicSite: N (2.309, 4.894, 2.86) [0.4467, 0.9467, 0.5533]
 PeriodicSite: N (4.894, 2.86, 2.309) [0.9467, 0.5533, 0.4467]
 PeriodicSite: N (2.86, 2.309, 4.894) [0.5533, 0.4467, 0.9467]
 PeriodicSite: N (0.2756, 0.2756, 0.2756) [0.0533, 0.0533, 0.0533]
 PeriodicSite: H (4.658, 5.029, 1.039) [0.9011, 0.9727, 0.2009]
 PeriodicSite: H (4.013, 2.973, 1.974) [0.7762, 0.5751, 0.3819]
 PeriodicSite: H (1.729, 4.65, 2.002) [0.3345, 0.8995, 0.3873]
 PeriodicSite: H (2.914, 3.283, 0.1321) [0.5636, 0.635, 0.02556]
 PeriodicSite: H (0.4254, 1.122, 0.5066) [0.08228, 0.217, 0.098]
 PeriodicSite: H (0.5707, 2.943, 2.357) [0.1104, 0.5693, 0.4559]
 PeriodicSite: H (3.371, 1.632, 0.07947) [0.6522, 0.3157, 0.01537]
 PeriodicSite: H (2.711, 4.801, 3.502) [0.5245, 0.9286, 0.6774]
 PeriodicSite: H (1.961, 2.167, 4.502) [0.3794, 0.4192, 0.8708]
 PeriodicSite: H (4.554, 2.437, 3.395) [0.881, 0.4715, 0.6567]
 PeriodicSite: H (0.263, 4.842, 4.726) [0.05087, 0.9365, 0.9142]
 PeriodicSite: H (2.051, 0.9003, 2.706) [0.3967, 0.1741, 0.5234],
 '47b9a869_9b1e_438b_8c93_f5ac654bfdd8': Structure Summary
 Lattice
     abc : 4.38880300521851 4.401448726654057 7.175978183746338
  angles : 90.000002504478 90.00000250447802 119.90499541135148
  volume : 120.16235834626013
       A : 4.388803005218506 0.0 -1.9184066957222967e-07
       B : -2.1944008875261014 3.8154102843847926 -1.9239342918808688e-07
       C : 0.0 0.0 7.175978183746338
     pbc : True True True
 PeriodicSite: O (2.194, 2.549, 3.886) [0.8341, 0.6681, 0.5415]
 PeriodicSite: O (2.041e-07, 1.266, 0.2978) [0.1659, 0.3319, 0.0415]
 PeriodicSite: O (2.194, 2.544, 6.579) [0.8334, 0.6667, 0.9168]
 PeriodicSite: O (2.05e-07, 1.272, 2.991) [0.1666, 0.3333, 0.4168]
 PeriodicSite: H (-0.00404, 1.27, 1.633) [0.1655, 0.3328, 0.2275]
 PeriodicSite: H (2.18, 2.575, 5.204) [0.8343, 0.6749, 0.7252]
 PeriodicSite: H (1.241, 2.012, 3.439) [0.5466, 0.5274, 0.4792]
 PeriodicSite: H (2.154, 3.561, 3.503) [0.9575, 0.9332, 0.4882]
 PeriodicSite: H (2.998, 2.102, 6.862) [0.9585, 0.5509, 0.9562]
 PeriodicSite: H (0.8265, 1.755, 7.096) [0.4183, 0.46, 0.9888]
 PeriodicSite: H (0.01103, 0.1311, 7.014) [0.01969, 0.03436, 0.9775]
 PeriodicSite: H (-0.7893, 1.721, 3.241) [0.04569, 0.4511, 0.4516],
 '662c7351_ee76_48ea_bab7_b733e1fdf607': Structure Summary
 Lattice
     abc : 4.167909392982183 8.414297301182946 8.41429615020752
  angles : 86.48328861312336 75.66042875469425 75.66042198607414
  volume : 276.98893913632514
       A : 4.038057804107666 0.0 1.0322586297988892
       B : 2.0190288528503957 8.152148872105393 0.5161301493644714
       C : 0.0 0.0 8.41429615020752
     pbc : True True True
 PeriodicSite: O (0.6612, 1.915, 6.606) [0.04627, 0.2349, 0.7651]
 PeriodicSite: O (4.326, 5.991, 3.336) [0.7037, 0.7349, 0.2651]
 PeriodicSite: O (1.732, 6.237, 2.419) [0.04627, 0.7651, 0.2349]
 PeriodicSite: O (3.377, 2.161, 7.047) [0.7037, 0.2651, 0.7349]
 PeriodicSite: O (3.377, 1.915, 2.84) [0.7188, 0.2349, 0.2349]
 PeriodicSite: O (3.751, 5.991, 7.143) [0.5613, 0.7349, 0.7349]
 PeriodicSite: O (2.307, 6.237, 7.027) [0.1887, 0.7651, 0.7651]
 PeriodicSite: O (0.6612, 2.161, 2.399) [0.03121, 0.2651, 0.2651]
 PeriodicSite: H (3.678, 2.716, 7.429) [0.7442, 0.3332, 0.7712]
 PeriodicSite: H (0.1682, 0.5427, 6.398) [0.008369, 0.06657, 0.7552]
 PeriodicSite: H (3.914, 6.039, 6.108) [0.5988, 0.7408, 0.607]
 PeriodicSite: H (5.223, 6.384, 3.671) [0.9019, 0.7831, 0.2776]
 PeriodicSite: H (4.78, 3.176, 3.444) [0.9889, 0.3895, 0.264]
 PeriodicSite: H (2.005, 2.087, 6.873) [0.3685, 0.256, 0.756]
 PeriodicSite: H (2.442, 6.189, 7.609) [0.2252, 0.7592, 0.8301]
 PeriodicSite: H (2.547, 1.818, 2.858) [0.5193, 0.223, 0.2622],
 '7fa282c5_4971_46f4_8b3b_776595a0fa06': Structure Summary
 Lattice
     abc : 6.332112789154059 6.332114696502691 6.603632926940918
  angles : 90.00000250447809 90.00000250447808 119.99999014147143
  volume : 229.303674421453
       A : 6.332112789154053 0.0 -2.767854425655969e-07
       B : -3.1660564046927258 5.483772731611829 -2.767855278307252e-07
       C : 0.0 0.0 6.603632926940918
     pbc : True True True
 PeriodicSite: Y (2.134, 0.0, 4.953) [0.3369, 0.0, 0.75]
 PeriodicSite: Y (1.067, 1.848, 1.651) [0.3369, 0.3369, 0.25]
 PeriodicSite: Y (-2.099, 3.636, 1.651) [6.806e-10, 0.6631, 0.25]
 PeriodicSite: Y (-1.067, 1.848, 4.953) [0.0, 0.3369, 0.75]
 PeriodicSite: Y (4.199, 4.059e-09, 1.651) [0.6631, 7.402e-10, 0.25]
 PeriodicSite: Y (2.099, 3.636, 4.953) [0.6631, 0.6631, 0.75]
 PeriodicSite: H (2.617, 4.687, 0.3188) [0.8406, 0.8547, 0.04828]
 PeriodicSite: H (3.336, 5.011, 4.241) [0.9836, 0.9138, 0.6422]
 PeriodicSite: H (1.738, 3.59, 0.5792) [0.6018, 0.6547, 0.0877]
 PeriodicSite: H (4.316, 0.07872, 5.541) [0.6888, 0.01435, 0.8391]
 PeriodicSite: H (-0.1905, 4.877, 0.4051) [0.4146, 0.8894, 0.06134]
 PeriodicSite: H (0.8336, 3.08, 3.427) [0.4125, 0.5617, 0.519]
 PeriodicSite: H (4.981, 1.859, 2.67) [0.9562, 0.339, 0.4044]
 PeriodicSite: H (2.164, 0.2364, 2.583) [0.3634, 0.04311, 0.3912]
 PeriodicSite: H (-1.189, 3.809, 3.433) [0.1596, 0.6946, 0.5199]
 PeriodicSite: H (3.06, 1.971, 1.342) [0.663, 0.3594, 0.2032]
 PeriodicSite: H (6.034, 0.05884, 3.022) [0.9583, 0.01073, 0.4576]
 PeriodicSite: H (3.116, 1.799, 4.557) [0.6561, 0.328, 0.69]
 PeriodicSite: H (1.331, 0.2379, 0.3926) [0.2319, 0.04337, 0.05945]
 PeriodicSite: H (0.2431, 3.149, 5.876) [0.3255, 0.5743, 0.8898]
 PeriodicSite: H (-1.052, 1.826, 0.5455) [0.0003599, 0.333, 0.08261]
 PeriodicSite: H (2.353, 4.268, 1.745) [0.7608, 0.7782, 0.2643]
 PeriodicSite: H (4.193, 3.567, 5.83) [0.9874, 0.6505, 0.8829]
 PeriodicSite: H (0.9715, 1.36, 4.971) [0.2774, 0.248, 0.7527],
 'c436bbf4_9aef_44a8_8960_00227f79a32f': Structure Summary
 Lattice
     abc : 4.403401374816899 4.962053775787357 5.689428329467773
  angles : 90.00000250447805 90.00000250447815 90.00000250447816
  volume : 124.31352208745227
       A : 4.4034013748168945 0.0 -1.924787937923611e-07
       B : -2.1689827722570944e-07 4.962053775787348 -2.1689825757675862e-07
       C : 0.0 0.0 5.689428329467773
     pbc : True True True
 PeriodicSite: V (2.02, 2.481, 1.451) [0.4587, 0.5, 0.2551]
 PeriodicSite: V (2.02, 4.962, 4.238) [0.4587, 1.0, 0.7449]
 PeriodicSite: V (2.02, 2.481, 4.238) [0.4587, 0.5, 0.7449]
 PeriodicSite: V (2.02, 2.13e-06, 1.451) [0.4587, 4.293e-07, 0.2551]
 PeriodicSite: V (4.251, 2.481, 2.845) [0.9654, 0.5, 0.5]
 PeriodicSite: V (4.251, 0.0, 2.845) [0.9654, 0.0, 0.5]
 PeriodicSite: V (4.243, 2.481, -2.939e-07) [0.9636, 0.5, 0.0]
 PeriodicSite: V (4.243, 0.0, -1.855e-07) [0.9636, 0.0, 0.0]
 PeriodicSite: H (2.721, 1.204, 5.614) [0.6179, 0.2427, 0.9868]
 PeriodicSite: H (2.758, 3.671, 2.776) [0.6263, 0.7399, 0.4878]
 PeriodicSite: H (0.8412, 3.666, 0.8015) [0.191, 0.7389, 0.1409]
 PeriodicSite: H (0.5002, 0.9219, 1.349) [0.1136, 0.1858, 0.2371]
 PeriodicSite: H (0.5522, 1.211, 4.23) [0.1254, 0.244, 0.7434]
 PeriodicSite: H (2.739, 1.2, 2.812) [0.6219, 0.2419, 0.4942]}

Relax structures¶

In [14]:

Copied!

from xtalpaint.utils.relaxation_utils import relax_structures
from xtalpaint.utils.relaxation_utils import relax_structures

In [15]:

Copied!





relax_kwargs = inputs.relaxation.relax_config.params.model_dump()
print(json.dumps(relax_kwargs, indent=4))

structure_labels, inpainted_structures = map(
    list,
    zip(
        *inpainting_outputs["structures"].get_structures(strct_type="pymatgen").items()
    ),
)

if inputs.relaxation.constrained:
    constrained_relaxation_outputs = relax_structures(
        structures=inpainted_structures,
        **relax_kwargs,
    )
if inputs.relaxation.full:
    relax_kwargs.pop("elements_to_relax", None)
    full_relaxation_outputs = relax_structures(
        structures=inpainted_structures,
        **relax_kwargs,
    )

constrained_relaxation_structures = dict(
    zip(structure_labels, constrained_relaxation_outputs[0])
)

full_relaxation_structures = dict(
    zip(structure_labels, full_relaxation_outputs[0])
)
relax_kwargs = inputs.relaxation.relax_config.params.model_dump()
print(json.dumps(relax_kwargs, indent=4))

structure_labels, inpainted_structures = map(
    list,
    zip(
        *inpainting_outputs["structures"].get_structures(strct_type="pymatgen").items()
    ),
)

if inputs.relaxation.constrained:
    constrained_relaxation_outputs = relax_structures(
        structures=inpainted_structures,
        **relax_kwargs,
    )
if inputs.relaxation.full:
    relax_kwargs.pop("elements_to_relax", None)
    full_relaxation_outputs = relax_structures(
        structures=inpainted_structures,
        **relax_kwargs,
    )

constrained_relaxation_structures = dict(
    zip(structure_labels, constrained_relaxation_outputs[0])
)

full_relaxation_structures = dict(
    zip(structure_labels, full_relaxation_outputs[0])
)

{
    "mlip": "mattersim",
    "optimizer": "BFGS",
    "load_path": "MatterSim-v1.0.0-5M.pth",
    "fmax": 0.01,
    "max_n_steps": 50,
    "max_natoms_per_batch": 5000,
    "device": "cpu",
    "filter": "none",
    "elements_to_relax": [
        "H"
    ],
    "return_initial_energies": false,
    "return_initial_forces": false,
    "return_final_forces": false
}
2026-06-17 11:16:50.461 | INFO     | mattersim.forcefield.potential:from_checkpoint:891 - Loading the pre-trained mattersim-v1.0.0-5M.pth model

  0%|          | 0/5 [00:00<?, ?it/s]

      Step     Time          Energy          fmax
BFGS:    0 11:16:50      -70.270988       27.396616
BFGS:    1 11:16:50      -74.499962        4.188519
BFGS:    2 11:16:51      -75.840904        2.985003
BFGS:    3 11:16:51      -76.635338        1.931414
BFGS:    4 11:16:51      -76.870506        1.655417
BFGS:    5 11:16:51      -77.599380        1.408866
BFGS:    6 11:16:51      -77.653534        0.954376
BFGS:    7 11:16:51      -77.693161        0.381834
BFGS:    8 11:16:52      -77.709312        0.459464
BFGS:    9 11:16:52      -77.753868        0.869609
BFGS:   10 11:16:52      -77.798302        1.220131
BFGS:   11 11:16:52      -77.849113        1.042157
BFGS:   12 11:16:52      -77.889221        0.804927
BFGS:   13 11:16:52      -77.960747        0.820123
BFGS:   14 11:16:52      -78.038101        1.401052
BFGS:   15 11:16:53      -78.114716        1.699412
BFGS:   16 11:16:53      -78.171371        1.321294
BFGS:   17 11:16:53      -78.213470        0.462264
BFGS:   18 11:16:53      -78.229034        0.596580
BFGS:   19 11:16:53      -78.248756        0.837303
BFGS:   20 11:16:53      -78.280769        0.750089
BFGS:   21 11:16:54      -78.315704        0.691908
BFGS:   22 11:16:54      -78.347260        0.572743
BFGS:   23 11:16:54      -78.378227        0.337961
BFGS:   24 11:16:54      -78.396248        0.349899
BFGS:   25 11:16:54      -78.417648        0.423497
BFGS:   26 11:16:54      -78.449387        0.516103
BFGS:   27 11:16:54      -78.484428        0.567460
BFGS:   28 11:16:55      -78.516083        0.535963
BFGS:   29 11:16:55      -78.528946        0.318997
BFGS:   30 11:16:55      -78.533272        0.226902
BFGS:   31 11:16:55      -78.538933        0.234223
BFGS:   32 11:16:55      -78.546989        0.250673
BFGS:   33 11:16:55      -78.557121        0.288306
BFGS:   34 11:16:55      -78.567680        0.260278
BFGS:   35 11:16:56      -78.579567        0.330458
BFGS:   36 11:16:56      -78.594017        0.360993
BFGS:   37 11:16:56      -78.615273        0.415380
BFGS:   38 11:16:56      -78.643738        0.486412
BFGS:   39 11:16:56      -78.675133        0.531067
BFGS:   40 11:16:56      -78.703560        0.507445
BFGS:   41 11:16:56      -78.704399        0.421231
BFGS:   42 11:16:57      -78.719551        0.339080
BFGS:   43 11:16:57      -78.724434        0.232848
BFGS:   44 11:16:57      -78.730240        0.170094
BFGS:   45 11:16:57      -78.743835        0.230980
BFGS:   46 11:16:57      -78.752136        0.275767
BFGS:   47 11:16:57      -78.758987        0.288545
BFGS:   48 11:16:58      -78.765289        0.271114
BFGS:   49 11:16:58      -78.774597        0.327832
BFGS:   50 11:16:58      -78.780411        0.241466
      Step     Time          Energy          fmax
BFGS:    0 11:16:58      -57.849968        2.499280
BFGS:    1 11:16:58      -57.997936        1.307911
BFGS:    2 11:16:58      -58.148010        1.143816
BFGS:    3 11:16:58      -58.335903        1.972952
BFGS:    4 11:16:58      -58.500576        2.992411
BFGS:    5 11:16:58      -58.890488        3.494797
BFGS:    6 11:16:58      -59.086906        4.293419
BFGS:    7 11:16:58      -59.298473        1.538319
BFGS:    8 11:16:58      -59.477882        1.084809
BFGS:    9 11:16:59      -59.517067        0.510377
BFGS:   10 11:16:59      -59.523624        0.256406
BFGS:   11 11:16:59      -59.528667        0.163155
BFGS:   12 11:16:59      -59.530540        0.199203
BFGS:   13 11:16:59      -59.532524        0.208748
BFGS:   14 11:16:59      -59.534428        0.149822
BFGS:   15 11:16:59      -59.535419        0.073244
BFGS:   16 11:16:59      -59.535828        0.063380
BFGS:   17 11:16:59      -59.536110        0.067042
BFGS:   18 11:16:59      -59.536373        0.053239
BFGS:   19 11:16:59      -59.536549        0.041333
BFGS:   20 11:16:59      -59.536636        0.032360
BFGS:   21 11:16:59      -59.536671        0.017327
BFGS:   22 11:16:59      -59.536694        0.012405
BFGS:   23 11:16:59      -59.536716        0.013821
BFGS:   24 11:17:00      -59.536736        0.016185
BFGS:   25 11:17:00      -59.536751        0.014503
BFGS:   26 11:17:00      -59.536766        0.012080
BFGS:   27 11:17:00      -59.536770        0.005163
      Step     Time          Energy          fmax
BFGS:    0 11:17:00      -35.723461       95.972805
BFGS:    1 11:17:00      -55.176739       22.468366
BFGS:    2 11:17:00      -60.281860       17.695452
BFGS:    3 11:17:00      -63.774815        6.509674
BFGS:    4 11:17:00      -65.524773        4.368346
BFGS:    5 11:17:00      -66.417969        3.489198
BFGS:    6 11:17:01      -66.898483        4.090190
BFGS:    7 11:17:01      -67.389977        3.553324
BFGS:    8 11:17:01      -68.222862        3.223622
BFGS:    9 11:17:01      -68.555466        3.023922
BFGS:   10 11:17:01      -68.784729        2.423833
BFGS:   11 11:17:01      -68.898743        1.852934
BFGS:   12 11:17:01      -69.085716        2.123425
BFGS:   13 11:17:01      -69.184860        2.098709
BFGS:   14 11:17:01      -69.431259        1.602771
BFGS:   15 11:17:02      -69.522766        1.166140
BFGS:   16 11:17:02      -69.602898        0.919815
BFGS:   17 11:17:02      -69.648590        1.200670
BFGS:   18 11:17:02      -69.710640        1.250082
BFGS:   19 11:17:02      -69.745186        0.905962
BFGS:   20 11:17:02      -69.778282        0.654941
BFGS:   21 11:17:02      -69.797661        0.394177
BFGS:   22 11:17:03      -69.808640        0.371837

  0%|          | 0/5 [00:12<?, ?it/s]

BFGS:   23 11:17:03      -69.813553        0.249655
BFGS:   24 11:17:03      -69.816299        0.253110
BFGS:   25 11:17:03      -69.818542        0.236869
BFGS:   26 11:17:03      -69.821152        0.202713
BFGS:   27 11:17:03      -69.824837        0.292975
BFGS:   28 11:17:03      -69.829674        0.332777
BFGS:   29 11:17:03      -69.834763        0.241037
BFGS:   30 11:17:03      -69.838509        0.167128
BFGS:   31 11:17:04      -69.840378        0.141676
BFGS:   32 11:17:04      -69.842255        0.155725
BFGS:   33 11:17:04      -69.845612        0.193301
BFGS:   34 11:17:04      -69.849098        0.154564
BFGS:   35 11:17:04      -69.851143        0.162770
BFGS:   36 11:17:04      -69.852547        0.175918
BFGS:   37 11:17:04      -69.853889        0.162832
BFGS:   38 11:17:04      -69.855293        0.172993
BFGS:   39 11:17:05      -69.857559        0.207092
BFGS:   40 11:17:05      -69.860382        0.299088
BFGS:   41 11:17:05      -69.862892        0.170201
BFGS:   42 11:17:05      -69.865059        0.199738
BFGS:   43 11:17:05      -69.867210        0.094614
BFGS:   44 11:17:05      -69.868217        0.115140
BFGS:   45 11:17:05      -69.869194        0.079481
BFGS:   46 11:17:05      -69.870552        0.115800
BFGS:   47 11:17:06      -69.872780        0.115226
BFGS:   48 11:17:06      -69.874634        0.241280
BFGS:   49 11:17:06      -69.874756        0.106068
BFGS:   50 11:17:06      -69.876114        0.116408

 60%|██████    | 3/5 [00:15<00:10,  5.26s/it]

      Step     Time          Energy          fmax
BFGS:    0 11:17:06     -105.523079        2.831747
BFGS:    1 11:17:06     -105.844795        2.502550
BFGS:    2 11:17:06     -106.931923        1.939379
BFGS:    3 11:17:06     -107.505806        2.209608
BFGS:    4 11:17:07     -107.877724        2.079734
BFGS:    5 11:17:07     -108.166786        1.732246
BFGS:    6 11:17:07     -108.438942        1.521069
BFGS:    7 11:17:07     -108.800812        1.320607
BFGS:    8 11:17:07     -109.387474        0.891212
BFGS:    9 11:17:07     -109.559525        1.089477
BFGS:   10 11:17:08     -109.638229        1.135089
BFGS:   11 11:17:08     -110.190552        0.786671
BFGS:   12 11:17:08     -110.328934        0.822952
BFGS:   13 11:17:08     -110.364540        0.737386
BFGS:   14 11:17:08     -110.422577        0.605793
BFGS:   15 11:17:08     -110.489090        0.514453
BFGS:   16 11:17:09     -110.579300        0.605557
BFGS:   17 11:17:09     -110.645714        0.529491
BFGS:   18 11:17:09     -110.683823        0.453183
BFGS:   19 11:17:09     -110.711540        0.427243
BFGS:   20 11:17:09     -110.768837        0.577145
BFGS:   21 11:17:09     -110.872879        0.814453
BFGS:   22 11:17:09     -110.968910        0.763779
BFGS:   23 11:17:09     -111.044731        0.652293
BFGS:   24 11:17:10     -111.124855        0.589010
BFGS:   25 11:17:10     -111.173698        0.555503
BFGS:   26 11:17:10     -111.272293        0.528761
BFGS:   27 11:17:10     -111.383286        0.581668
BFGS:   28 11:17:10     -111.495361        0.675660
BFGS:   29 11:17:10     -111.554718        0.673314
BFGS:   30 11:17:11     -111.611916        0.720092
BFGS:   31 11:17:11     -111.649765        0.715665
BFGS:   32 11:17:11     -111.802414        0.689973
BFGS:   33 11:17:11     -111.959396        0.664390
BFGS:   34 11:17:11     -112.081741        0.672248
BFGS:   35 11:17:11     -112.174049        0.722953
BFGS:   36 11:17:12     -112.226456        0.726625
BFGS:   37 11:17:12     -112.276077        0.671088
BFGS:   38 11:17:12     -112.345863        0.529722
BFGS:   39 11:17:12     -112.438988        0.370384
BFGS:   40 11:17:12     -112.523056        0.317759
BFGS:   41 11:17:12     -112.562469        0.260313
BFGS:   42 11:17:12     -112.575676        0.251621
BFGS:   43 11:17:12     -112.589264        0.250523
BFGS:   44 11:17:13     -112.612564        0.241452
BFGS:   45 11:17:13     -112.640236        0.205214
BFGS:   46 11:17:13     -112.658691        0.166591
BFGS:   47 11:17:13     -112.665771        0.164321
BFGS:   48 11:17:13     -112.669815        0.161421
BFGS:   49 11:17:13     -112.676201        0.144267
BFGS:   50 11:17:13     -112.686127        0.127883

 80%|████████  | 4/5 [00:23<00:05,  5.94s/it]

      Step     Time          Energy          fmax
BFGS:    0 11:17:13      -89.740555        1.018145
BFGS:    1 11:17:13      -89.759506        0.961740
BFGS:    2 11:17:13      -89.908768        0.339078
BFGS:    3 11:17:14      -89.921295        0.432801
BFGS:    4 11:17:14      -89.926529        0.429793
BFGS:    5 11:17:14      -89.934753        0.320503
BFGS:    6 11:17:14      -89.940468        0.196779
BFGS:    7 11:17:14      -89.943199        0.211108
BFGS:    8 11:17:14      -89.944702        0.250088
BFGS:    9 11:17:14      -89.947868        0.314953
BFGS:   10 11:17:14      -89.956642        0.451185
BFGS:   11 11:17:14      -89.982475        0.724945
BFGS:   12 11:17:14      -90.004456        0.726012
BFGS:   13 11:17:15      -90.037994        0.699782
BFGS:   14 11:17:15      -90.088318        0.579491
BFGS:   15 11:17:15      -90.114799        0.459431
BFGS:   16 11:17:15      -90.135254        0.387353
BFGS:   17 11:17:15      -90.152138        0.458728
BFGS:   18 11:17:15      -90.170982        0.392503
BFGS:   19 11:17:15      -90.191521        0.286286
BFGS:   20 11:17:15      -90.202827        0.184861
BFGS:   21 11:17:15      -90.206558        0.157829
BFGS:   22 11:17:16      -90.207909        0.138924
BFGS:   23 11:17:16      -90.210129        0.114042
BFGS:   24 11:17:16      -90.214005        0.088605
BFGS:   25 11:17:16      -90.217720        0.062381
BFGS:   26 11:17:16      -90.219215        0.041981
BFGS:   27 11:17:16      -90.219536        0.041047
BFGS:   28 11:17:16      -90.219627        0.036217
BFGS:   29 11:17:16      -90.219742        0.028476
BFGS:   30 11:17:16      -90.219917        0.021621
BFGS:   31 11:17:16      -90.220070        0.014947
BFGS:   32 11:17:17      -90.220123        0.010757
BFGS:   33 11:17:17      -90.220116        0.008424

100%|██████████| 5/5 [00:26<00:00,  5.31s/it]

2026-06-17 11:17:17.117 | INFO     | mattersim.forcefield.potential:from_checkpoint:891 - Loading the pre-trained mattersim-v1.0.0-5M.pth model

  0%|          | 0/5 [00:00<?, ?it/s]

      Step     Time          Energy          fmax
BFGS:    0 11:17:17      -70.270988       33.654266
BFGS:    1 11:17:17      -75.354149       13.886686
BFGS:    2 11:17:17      -76.499237        6.433766
BFGS:    3 11:17:17      -77.296906        2.663641
BFGS:    4 11:17:18      -77.546814        1.823530
BFGS:    5 11:17:18      -77.882584        1.747173
BFGS:    6 11:17:18      -78.001740        1.108277
BFGS:    7 11:17:18      -78.119026        1.345996
BFGS:    8 11:17:18      -78.193146        1.190743
BFGS:    9 11:17:18      -78.316040        1.618791
BFGS:   10 11:17:18      -78.394241        1.413521
BFGS:   11 11:17:19      -78.483047        0.935703
BFGS:   12 11:17:19      -78.509010        0.702104
BFGS:   13 11:17:19      -78.527298        0.460736
BFGS:   14 11:17:19      -78.544472        0.587034
BFGS:   15 11:17:19      -78.559311        0.512003
BFGS:   16 11:17:19      -78.569069        0.280085
BFGS:   17 11:17:20      -78.578842        0.360425
BFGS:   18 11:17:20      -78.595238        0.764597
BFGS:   19 11:17:20      -78.627815        1.252886
BFGS:   20 11:17:20      -78.676651        1.341499
BFGS:   21 11:17:20      -78.720268        0.821468
BFGS:   22 11:17:20      -78.754311        0.290948
BFGS:   23 11:17:20      -78.762856        0.336341
BFGS:   24 11:17:21      -78.769707        0.403450
BFGS:   25 11:17:21      -78.776413        0.322271
BFGS:   26 11:17:21      -78.782425        0.192575
BFGS:   27 11:17:21      -78.786301        0.161942
BFGS:   28 11:17:21      -78.792465        0.237191
BFGS:   29 11:17:21      -78.804428        0.424805
BFGS:   30 11:17:21      -78.828331        0.546115
BFGS:   31 11:17:22      -78.858238        0.519679
BFGS:   32 11:17:22      -78.880241        0.425775
BFGS:   33 11:17:22      -78.875114        0.961343
BFGS:   34 11:17:22      -78.895538        0.212346
BFGS:   35 11:17:22      -78.897873        0.261533
BFGS:   36 11:17:22      -78.900139        0.198327
BFGS:   37 11:17:22      -78.905205        0.086386
BFGS:   38 11:17:23      -78.906136        0.092917
BFGS:   39 11:17:23      -78.908852        0.136596
BFGS:   40 11:17:23      -78.912582        0.209937
BFGS:   41 11:17:23      -78.919617        0.353707
BFGS:   42 11:17:23      -78.927254        0.420725
BFGS:   43 11:17:23      -78.934235        0.366803
BFGS:   44 11:17:24      -78.940483        0.221704
BFGS:   45 11:17:24      -78.945702        0.223064
BFGS:   46 11:17:24      -78.951195        0.128149
BFGS:   47 11:17:24      -78.954468        0.174074
BFGS:   48 11:17:24      -78.955948        0.125883
BFGS:   49 11:17:24      -78.957184        0.094297
BFGS:   50 11:17:24      -78.959076        0.119806
      Step     Time          Energy          fmax
BFGS:    0 11:17:25      -57.849968        4.278671
BFGS:    1 11:17:25      -58.266541        1.680875
BFGS:    2 11:17:25      -58.547195        1.658323
BFGS:    3 11:17:25      -58.028492        7.881478
BFGS:    4 11:17:25      -58.954895        1.489440
BFGS:    5 11:17:25      -59.120483        1.370929
BFGS:    6 11:17:25      -59.139610        2.557338
BFGS:    7 11:17:25      -59.271072        0.894278
BFGS:    8 11:17:25      -59.310143        0.698286
BFGS:    9 11:17:25      -59.414368        1.141939
BFGS:   10 11:17:25      -59.449505        0.422270
BFGS:   11 11:17:25      -59.469799        0.391759
BFGS:   12 11:17:25      -59.489799        0.513454
BFGS:   13 11:17:25      -59.510513        0.468838
BFGS:   14 11:17:26      -59.521011        0.184787
BFGS:   15 11:17:26      -59.523968        0.149171
BFGS:   16 11:17:26      -59.526215        0.164407
BFGS:   17 11:17:26      -59.529274        0.187168
BFGS:   18 11:17:26      -59.531857        0.139145
BFGS:   19 11:17:26      -59.533260        0.076764
BFGS:   20 11:17:26      -59.533928        0.065385
BFGS:   21 11:17:26      -59.534607        0.102295
BFGS:   22 11:17:26      -59.535534        0.119213
BFGS:   23 11:17:26      -59.536312        0.079531
BFGS:   24 11:17:26      -59.536629        0.031283
BFGS:   25 11:17:26      -59.536709        0.022459
BFGS:   26 11:17:26      -59.536758        0.023241
BFGS:   27 11:17:26      -59.536804        0.020650
BFGS:   28 11:17:26      -59.536842        0.015053
BFGS:   29 11:17:27      -59.536858        0.013903
BFGS:   30 11:17:27      -59.536884        0.012969
BFGS:   31 11:17:27      -59.536907        0.015479
BFGS:   32 11:17:27      -59.536926        0.010014
BFGS:   33 11:17:27      -59.536930        0.005493
      Step     Time          Energy          fmax
BFGS:    0 11:17:27      -35.723461       95.972805
BFGS:    1 11:17:27      -60.766048       12.583023
BFGS:    2 11:17:27      -64.706650        7.043029
BFGS:    3 11:17:27      -67.242165        4.795914
BFGS:    4 11:17:27      -68.549805       11.357987
BFGS:    5 11:17:28      -69.515533        3.183407
BFGS:    6 11:17:28      -69.973190        2.700315
BFGS:    7 11:17:28      -70.319916        2.287087
BFGS:    8 11:17:28      -70.546478        2.377600
BFGS:    9 11:17:28      -70.966782        2.552471
BFGS:   10 11:17:28      -71.163010        2.462399
BFGS:   11 11:17:28      -71.646339        2.546768
BFGS:   12 11:17:28      -71.832649        1.627594
BFGS:   13 11:17:28      -71.992928        1.188777
BFGS:   14 11:17:28      -72.042931        0.623719
BFGS:   15 11:17:29      -72.059586        0.356909
BFGS:   16 11:17:29      -72.069191        0.343234
BFGS:   17 11:17:29      -72.084793        0.266054
BFGS:   18 11:17:29      -72.092445        0.299569
BFGS:   19 11:17:29      -72.102554        0.365456
BFGS:   20 11:17:29      -72.116829        0.483358
BFGS:   21 11:17:29      -72.139442        0.526568
BFGS:   22 11:17:29      -72.165253        0.617671
BFGS:   23 11:17:30      -72.192085        0.503062
BFGS:   24 11:17:30      -72.212265        0.374284
BFGS:   25 11:17:30      -72.228050        0.357620
BFGS:   26 11:17:30      -72.243034        0.376609
BFGS:   27 11:17:30      -72.256653        0.368446
BFGS:   28 11:17:30      -72.266129        0.329704
BFGS:   29 11:17:30      -72.273567        0.330749
BFGS:   30 11:17:30      -72.281830        0.359018
BFGS:   31 11:17:30      -72.291809        0.379213
BFGS:   32 11:17:31      -72.299629        0.395540
BFGS:   33 11:17:31      -72.308983        0.412334
BFGS:   34 11:17:31      -72.319000        0.358986
BFGS:   35 11:17:31      -72.335571        0.397576
BFGS:   36 11:17:31      -72.353416        0.383761
BFGS:   37 11:17:31      -72.361153        0.227649
BFGS:   38 11:17:31      -72.358215        0.644601
BFGS:   39 11:17:31      -72.370918        0.198993
BFGS:   40 11:17:32      -72.373840        0.168167
BFGS:   41 11:17:32      -72.385735        0.227893
BFGS:   42 11:17:32      -72.390152        0.236584
BFGS:   43 11:17:32      -72.395760        0.175714
BFGS:   44 11:17:32      -72.401344        0.162447
BFGS:   45 11:17:32      -72.410851        0.213107
BFGS:   46 11:17:32      -72.423592        0.269272
BFGS:   47 11:17:32      -72.434692        0.256062
BFGS:   48 11:17:33      -72.443947        0.260208

  0%|          | 0/5 [00:15<?, ?it/s]

BFGS:   49 11:17:33      -72.450127        0.264281
BFGS:   50 11:17:33      -72.456390        0.266553

 60%|██████    | 3/5 [00:15<00:10,  5.33s/it]

      Step     Time          Energy          fmax
BFGS:    0 11:17:33     -105.523079        3.432754
BFGS:    1 11:17:33     -106.166115        2.408582
BFGS:    2 11:17:33     -107.573738        1.823864
BFGS:    3 11:17:33     -107.956886        1.714533
BFGS:    4 11:17:33     -108.349243        1.795668
BFGS:    5 11:17:34     -108.756203        1.767675
BFGS:    6 11:17:34     -109.334709        2.232100
BFGS:    7 11:17:34     -109.814568        1.443421
BFGS:    8 11:17:34     -110.009705        1.346202
BFGS:    9 11:17:34     -110.223221        1.469743
BFGS:   10 11:17:34     -110.475517        0.836307
BFGS:   11 11:17:35     -110.599747        0.775197
BFGS:   12 11:17:35     -110.694786        0.813894
BFGS:   13 11:17:35     -110.804352        1.206672
BFGS:   14 11:17:35     -110.940735        1.256352
BFGS:   15 11:17:35     -111.056351        0.849995
BFGS:   16 11:17:35     -111.138298        0.625066
BFGS:   17 11:17:36     -111.199532        0.622593
BFGS:   18 11:17:36     -111.265633        0.695929
BFGS:   19 11:17:36     -111.349724        0.664430
BFGS:   20 11:17:36     -111.416824        0.559725
BFGS:   21 11:17:36     -111.476120        0.710503
BFGS:   22 11:17:36     -111.549065        0.740083
BFGS:   23 11:17:36     -111.649788        1.021406
BFGS:   24 11:17:36     -111.769569        1.106260
BFGS:   25 11:17:37     -111.885094        0.803114
BFGS:   26 11:17:37     -112.016747        1.062398
BFGS:   27 11:17:37     -112.145874        1.125907
BFGS:   28 11:17:37     -112.303963        1.146251
BFGS:   29 11:17:37     -112.448265        1.150485
BFGS:   30 11:17:37     -112.547012        0.790716
BFGS:   31 11:17:38     -112.630737        0.601625
BFGS:   32 11:17:38     -112.686310        0.437320
BFGS:   33 11:17:38     -112.777634        0.626547
BFGS:   34 11:17:38     -112.859543        0.697186
BFGS:   35 11:17:38     -112.917702        0.644482
BFGS:   36 11:17:38     -112.951393        0.500299
BFGS:   37 11:17:38     -112.991165        0.376208
BFGS:   38 11:17:39     -113.028358        0.420415
BFGS:   39 11:17:39     -113.051514        0.374849
BFGS:   40 11:17:39     -113.065041        0.366807
BFGS:   41 11:17:39     -113.079735        0.322226
BFGS:   42 11:17:39     -113.096695        0.242652
BFGS:   43 11:17:39     -113.110191        0.205401
BFGS:   44 11:17:40     -113.117828        0.168209
BFGS:   45 11:17:40     -113.123161        0.150407
BFGS:   46 11:17:40     -113.129982        0.169855
BFGS:   47 11:17:40     -113.138496        0.192494
BFGS:   48 11:17:40     -113.145462        0.165020
BFGS:   49 11:17:40     -113.149811        0.165275
BFGS:   50 11:17:40     -113.153854        0.134489

 80%|████████  | 4/5 [00:23<00:06,  6.12s/it]

      Step     Time          Energy          fmax
BFGS:    0 11:17:41      -89.740555        1.018145
BFGS:    1 11:17:41      -89.785698        0.899092
BFGS:    2 11:17:41      -89.925972        0.393973
BFGS:    3 11:17:41      -89.937485        0.318037
BFGS:    4 11:17:41      -89.954010        0.364299
BFGS:    5 11:17:41      -89.980286        0.383805
BFGS:    6 11:17:41      -90.009544        0.476963
BFGS:    7 11:17:41      -90.035263        0.532700
BFGS:    8 11:17:41      -90.097565        0.765820
BFGS:    9 11:17:42      -90.188324        1.297597
BFGS:   10 11:17:42      -90.335335        2.784432
BFGS:   11 11:17:42      -90.618477        2.115944
BFGS:   12 11:17:42      -91.453384        1.925646
BFGS:   13 11:17:42      -91.810699        1.941381
BFGS:   14 11:17:42      -92.049194        1.593175
BFGS:   15 11:17:42      -92.276848        1.111158
BFGS:   16 11:17:42      -92.597099        0.975584
BFGS:   17 11:17:42      -92.908279        1.590694
BFGS:   18 11:17:42      -93.054123        1.488075
BFGS:   19 11:17:42      -93.473404        1.012016
BFGS:   20 11:17:43      -93.574165        0.724807
BFGS:   21 11:17:43      -93.624832        0.511725
BFGS:   22 11:17:43      -93.678215        0.425377
BFGS:   23 11:17:43      -93.704514        0.259703
BFGS:   24 11:17:43      -93.716309        0.301754
BFGS:   25 11:17:43      -93.728935        0.310537
BFGS:   26 11:17:43      -93.741478        0.237774
BFGS:   27 11:17:43      -93.750328        0.197206
BFGS:   28 11:17:43      -93.755913        0.160661
BFGS:   29 11:17:44      -93.760590        0.177235
BFGS:   30 11:17:44      -93.765442        0.160820
BFGS:   31 11:17:44      -93.769608        0.145272
BFGS:   32 11:17:44      -93.772491        0.146689
BFGS:   33 11:17:44      -93.774712        0.113315
BFGS:   34 11:17:44      -93.776611        0.114134
BFGS:   35 11:17:44      -93.777985        0.090253
BFGS:   36 11:17:44      -93.778915        0.087169
BFGS:   37 11:17:44      -93.779701        0.069063
BFGS:   38 11:17:44      -93.780403        0.055734
BFGS:   39 11:17:44      -93.780998        0.056928
BFGS:   40 11:17:45      -93.781555        0.068079
BFGS:   41 11:17:45      -93.782249        0.088218
BFGS:   42 11:17:45      -93.783279        0.101505
BFGS:   43 11:17:45      -93.784630        0.097131
BFGS:   44 11:17:45      -93.786171        0.097765
BFGS:   45 11:17:45      -93.787872        0.109577
BFGS:   46 11:17:45      -93.789917        0.112443
BFGS:   47 11:17:45      -93.792587        0.129934
BFGS:   48 11:17:45      -93.796371        0.168810
BFGS:   49 11:17:45      -93.801910        0.206906
BFGS:   50 11:17:46      -93.808403        0.266281

100%|██████████| 5/5 [00:28<00:00,  5.76s/it]

Evaluate the inpainted structures with repspect to the initial reference¶

In [16]:

Copied!

from xtalpaint.eval import evaluate_inpainting
import pandas as pd
from xtalpaint.eval import evaluate_inpainting
import pandas as pd

In [17]:

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rmsd_inpainted_structures = evaluate_inpainting(
    inpainted_structures=inpainting_outputs["structures"],
    reference_structures=input_structures,
    metric="rmsd",
    max_workers=3,
    normalization_element='H',
)

matches_inpainted_structures = evaluate_inpainting(
    inpainted_structures=inpainting_outputs["structures"],
    reference_structures=input_structures,
    metric="match",
    max_workers=3,
)

inpainted_evaluation = pd.merge(
    rmsd_inpainted_structures, matches_inpainted_structures, left_index=True, right_index=True
)

rmsd_constrained_relaxation = evaluate_inpainting(
    inpainted_structures=constrained_relaxation_structures,
    reference_structures=input_structures,
    metric="rmsd",
    max_workers=3,
    normalization_element='H',
)
matches_constrained_relaxation = evaluate_inpainting(
    inpainted_structures=constrained_relaxation_structures,
    reference_structures=input_structures,
    metric="match",
    max_workers=3,
)

constrained_relaxation_evaluation = pd.merge(
    rmsd_constrained_relaxation, matches_constrained_relaxation, left_index=True, right_index=True
)
rmsd_inpainted_structures = evaluate_inpainting(
    inpainted_structures=inpainting_outputs["structures"],
    reference_structures=input_structures,
    metric="rmsd",
    max_workers=3,
    normalization_element='H',
)

matches_inpainted_structures = evaluate_inpainting(
    inpainted_structures=inpainting_outputs["structures"],
    reference_structures=input_structures,
    metric="match",
    max_workers=3,
)

inpainted_evaluation = pd.merge(
    rmsd_inpainted_structures, matches_inpainted_structures, left_index=True, right_index=True
)

rmsd_constrained_relaxation = evaluate_inpainting(
    inpainted_structures=constrained_relaxation_structures,
    reference_structures=input_structures,
    metric="rmsd",
    max_workers=3,
    normalization_element='H',
)
matches_constrained_relaxation = evaluate_inpainting(
    inpainted_structures=constrained_relaxation_structures,
    reference_structures=input_structures,
    metric="match",
    max_workers=3,
)

constrained_relaxation_evaluation = pd.merge(
    rmsd_constrained_relaxation, matches_constrained_relaxation, left_index=True, right_index=True
)

 80%|████████  | 4/5 [00:00<00:00, 14.41it/s]
 80%|████████  | 4/5 [00:00<00:00, 30.12it/s]
 80%|████████  | 4/5 [00:00<00:00, 15.30it/s]
 80%|████████  | 4/5 [00:00<00:00, 31.03it/s]

In [18]:

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inpainted_evaluation
inpainted_evaluation

Out[18]:

	rmsd	match
keys
20acc66e_8e38_4e5e_9e7a_c2400262cdc8	0.823770	False
47b9a869_9b1e_438b_8c93_f5ac654bfdd8	0.182364	True
662c7351_ee76_48ea_bab7_b733e1fdf607	1.808948	False
7fa282c5_4971_46f4_8b3b_776595a0fa06	0.922381	False
c436bbf4_9aef_44a8_8960_00227f79a32f	1.243808	False

In [19]:

Copied!

constrained_relaxation_evaluation
constrained_relaxation_evaluation

Out[19]:

	rmsd	match
keys
20acc66e_8e38_4e5e_9e7a_c2400262cdc8	0.778736	False
47b9a869_9b1e_438b_8c93_f5ac654bfdd8	0.009466	True
662c7351_ee76_48ea_bab7_b733e1fdf607	1.777973	False
7fa282c5_4971_46f4_8b3b_776595a0fa06	0.575861	False
c436bbf4_9aef_44a8_8960_00227f79a32f	1.408238	False