Water on NaCl surface¶

Set up environment (optional)¶

These steps are required for Google Colab, but may work on other systems too:

[1]:

#import locale
#locale.getpreferredencoding = lambda: "UTF-8"
#!python3 -m pip install pack-mm data-tutorials weas-widget

let us start by creating a box of NaCl with vaccum

[2]:

from weas_widget import WeasWidget
from ase.build import bulk

NaCl = bulk("NaCl", "rocksalt", a=5.61, cubic=True)
NaCl_super = NaCl*(3,3,3)
cell = NaCl_super.get_cell()
cell[2] *=3
NaCl_super.set_cell(cell)
NaCl_super.center()
viewer = WeasWidget()

indert_centre = (8.5, 8.5, 37)
a = 16.9
b = 16.9
c = 7

box= [{
    "type":"cube",
    "materialType": "Standard",
    "opacity": 0.25,
    "shape": {
        "width": a,
        "height": b,
        "depth": c,
        "widthSegments": 32,
        "heightSegments": 32,
        "depthSegments": 32,
      },
    "instances": [{
        "position": indert_centre,
        "scale": [1, 1, 1],
        "rotation": [0, 0, 0],
        "color": "#0000ff",
        }]
    }]

viewer.from_ase(NaCl_super)
viewer.avr.model_style = 1
viewer.imp.settings = box
viewer

[2]:

[3]:

from pack_mm.core.core import pack_molecules

e, final = pack_molecules(
        system=NaCl_super,
        molecule="H2O",
        nmols=20,
        arch="mace_mp",
        model="small-0b2",
        device="cpu",
        where="box",
        center=indert_centre,
        a=a,
        b=b,
        c=c,
        seed=2042,
        temperature=300,
        ntries=20,
        threshold=0.5,
        geometry=False,
        )

Inserting 20 H2O molecules in Cl108Na108+.
    Using mace_mp model small-0b2 on cpu.
    Insert in box.

/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/e3nn/o3/_wigner.py:10: UserWarning: Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected, since the`weights_only` argument was not explicitly passed to `torch.load`, forcing weights_only=False.
  _Jd, _W3j_flat, _W3j_indices = torch.load(os.path.join(os.path.dirname(__file__), 'constants.pt'))

cuequivariance or cuequivariance_torch is not available. Cuequivariance acceleration will be disabled.
Using Materials Project MACE for MACECalculator with /home/runner/.cache/mace/macesmalldensityagnesistressmodel
Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization.
Using head default out of ['default']

/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/mace/calculators/mace.py:197: UserWarning: Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected, since the`weights_only` argument was not explicitly passed to `torch.load`, forcing weights_only=False.
  torch.load(f=model_path, map_location=device)

Old energy=-722.6495705816244, new energy=-736.819502877273, de=-14.16993229564855, acc=np.float64(1.1078127747888251e+238), random=0.9224082858823739
Inserted particle 1
Old energy=-736.819502877273, new energy=-750.9822274031394, de=-14.162724525866452, acc=np.float64(8.382645971765483e+237), random=0.49465704267998434
Inserted particle 2
Old energy=-750.9822274031394, new energy=-765.1891028647847, de=-14.206875461645268, acc=np.float64(4.624709450717762e+238), random=0.9374033072986
Inserted particle 3
Old energy=-765.1891028647847, new energy=-779.3590112922313, de=-14.169908427446671, acc=np.float64(1.106790443609027e+238), random=0.11301187136860802
Inserted particle 4
Old energy=-779.3590112922313, new energy=-789.2676329985507, de=-9.908621706319309, acc=np.float64(2.8679720010572092e+166), random=0.6368663379349846
Inserted particle 5
Old energy=-789.2676329985507, new energy=-803.469210060474, de=-14.20157706192333, acc=np.float64(3.7676905441691194e+238), random=0.039025507402559945
Inserted particle 6
Old energy=-803.469210060474, new energy=-817.6176589775163, de=-14.148448917042288, acc=np.float64(4.8257116750036385e+237), random=0.7816264095523812
Inserted particle 7
Old energy=-817.6176589775163, new energy=-831.3717199695861, de=-13.754060992069867, acc=np.float64(1.1432299285991774e+231), random=0.7946384160766508
Inserted particle 8
Old energy=-831.3717199695861, new energy=-845.5508387418474, de=-14.17911877226129, acc=np.float64(1.5804924882978555e+238), random=0.3018355440106446
Inserted particle 9
Old energy=-845.5508387418474, new energy=-859.8440321607758, de=-14.293193418928354, acc=np.float64(1.3036553936042903e+240), random=0.8610063339435549
Inserted particle 10
Old energy=-859.8440321607758, new energy=-873.9735194901638, de=-14.129487329387985, acc=np.float64(2.3175046243855625e+237), random=0.8710374922225326
Inserted particle 11
Old energy=-873.9735194901638, new energy=-888.3900103944591, de=-14.416490904295301, acc=np.float64(1.5362790176203024e+242), random=0.9372407961015686
Inserted particle 12
Old energy=-888.3900103944591, new energy=-902.6369589400576, de=-14.24694854559857, acc=np.float64(2.1791286108073626e+239), random=0.8108197601233099
Inserted particle 13
Old energy=-902.6369589400576, new energy=-916.9585304149657, de=-14.321571474908069, acc=np.float64(3.907449067569078e+240), random=0.44068985410214423
Inserted particle 14
Old energy=-916.9585304149657, new energy=-931.2062273604676, de=-14.247696945501843, acc=np.float64(2.2431351048164295e+239), random=0.8847889911084612
Inserted particle 15
Old energy=-931.2062273604676, new energy=-932.3490353975458, de=-1.1428080370782254, acc=np.float64(1.5788343527977978e+19), random=0.2117478385102951
Old energy=-931.2062273604676, new energy=-945.3494484228157, de=-14.143221062348175, acc=np.float64(3.9421872317303134e+237), random=0.8188187672234769
Inserted particle 16
Old energy=-945.3494484228157, new energy=-959.5835928934794, de=-14.234144470663637, acc=np.float64(1.3279563438766754e+239), random=0.2555871566261533
Inserted particle 17
Old energy=-959.5835928934794, new energy=-973.7830515113416, de=-14.199458617862206, acc=np.float64(3.471258204501571e+238), random=0.5587630356823694
Inserted particle 18
Old energy=-973.7830515113416, new energy=-987.7693746278163, de=-13.98632311647475, acc=np.float64(9.119412679358459e+234), random=0.807305293242636
Inserted particle 19
Old energy=-987.7693746278163, new energy=-999.3733863713765, de=-11.604011743560136, acc=np.float64(8.687276785525228e+194), random=0.6110986123209559
Inserted particle 20

[4]:

viewer2=WeasWidget()
viewer2.from_ase(final)
viewer2.avr.model_style = 1
viewer2.avr.show_hydrogen_bonds = True
viewer2.imp.settings = box
viewer2

[4]: