Interfaces#
Atomic Simulation Environment#
We provide a calculator for Atomic Simulation Environment (ASE) that enables many routines such as optimization and molecular dynamics.
Examples#
Periodic box optimization#
import os
import numpy as np
from ase import Atoms
from ase.optimize import BFGS
from reptar.utils import parse_xyz
from reptar.writers import write_xyz
from mbgdml.interfaces.ase import mbeCalculator
from mbgdml.mbe import mbePredict
from mbgdml.models import gdmlModel
from mbgdml.periodic import Cell
from mbgdml.predictors import predict_gdml
from mbgdml.descriptors import Criteria, com_distance_sum
from mbgdml.utils import get_entity_ids, get_comp_ids, atoms_by_number
# Ensures we execute from script directory (for relative paths).
WORK_DIR = os.path.dirname(os.path.realpath(__file__))
os.chdir(WORK_DIR)
# Conversion factors.
HARTREE_TO_KCALMOL = 627.5094737775374055927342256 # Psi4 constant
HARTREE_TO_EV = 27.21138602 # Psi4 constant
EV_TO_KCALMOL = HARTREE_TO_KCALMOL / HARTREE_TO_EV
KCALMOL_TO_EV = HARTREE_TO_EV / HARTREE_TO_KCALMOL
print("Setting up system")
XYZ_PATH = "./33h2o.xyz"
Z, _, R = parse_xyz(XYZ_PATH)
Z = atoms_by_number(Z[0])
Z = np.array(Z)
R = np.array(R)
# Eventually we will make an ASE Atoms object that requires only a single structure.
if R.ndim == 3:
R = R[-1]
# Setup unit cell
BOX_LENGTH = 10.0 # Angstroms
MIC_CUTOFF = 5.0 # Maximum value is half of the box length
cell_v = [[BOX_LENGTH, 0.0, 0.0], [0.0, BOX_LENGTH, 0.0], [0.0, 0.0, BOX_LENGTH]]
periodic_cell = Cell(cell_v, pbc=True, cutoff=MIC_CUTOFF)
# Setup fragments
N_MOLECULES = 33
entity_ids = get_entity_ids(atoms_per_mol=3, num_mol=N_MOLECULES)
comp_ids = get_comp_ids(label="h2o", num_mol=N_MOLECULES)
# Setup ray.
# Note, this assumes you already ran `ray start --head` on your system's terminal.
N_WORKERS = 8 # Generally the number of CPU cores to use.
print("Setting up mbGDML")
model_paths = [
"./1h2o-model-gdml.npz",
"./2h2o-model-gdml-nbody.npz",
"./3h2o-model-gdml-nbody.npz",
]
model_comp_ids = [["h2o"], ["h2o", "h2o"], ["h2o", "h2o", "h2o"]]
model_desc_kwargs = (
{"entity_ids": get_entity_ids(atoms_per_mol=3, num_mol=1)},
{"entity_ids": get_entity_ids(atoms_per_mol=3, num_mol=2)},
{"entity_ids": get_entity_ids(atoms_per_mol=3, num_mol=3)},
)
model_desc_cutoffs = (None, 6.0, 10.0)
model_criteria = [
Criteria(com_distance_sum, desc_kwargs, cutoff)
for desc_kwargs, cutoff in zip(model_desc_kwargs, model_desc_cutoffs)
]
models = [
gdmlModel(path, comp_ids=model_comp_id, criteria=criteria)
for path, model_comp_id, criteria in zip(
model_paths, model_comp_ids, model_criteria
)
]
mbe_pred = mbePredict(
models, predict_gdml, use_ray=True, n_workers=N_WORKERS,
periodic_cell=periodic_cell
)
print("Setting up ASE")
ase_atoms = Atoms(numbers=Z, positions=R, cell=cell_v, pbc=True)
# Attach ASE calculator
mbe_calc = mbeCalculator(mbe_pred, e_conv=KCALMOL_TO_EV, f_conv=KCALMOL_TO_EV)
mbe_calc.directory = WORK_DIR
mbe_calc.set(entity_ids=entity_ids, comp_ids=comp_ids)
ase_atoms.calc = mbe_calc
# Setup logging
mbe_traj_path = os.path.join(WORK_DIR, "33h2o-opt.traj")
print("Starting optimization")
dyn = BFGS(atoms=ase_atoms, trajectory=mbe_traj_path)
dyn.run(fmax=0.4, steps=100)
print("Writing XYZ file")
Z = ase_atoms.get_atomic_numbers()
R = ase_atoms.get_positions()
write_xyz(os.path.join(WORK_DIR, "33h2o-opt.xyz"), Z, R[None, ...])
print("Done!")
Setting up system
Setting up mbGDML
2022-12-29 10:35:57,757 INFO worker.py:1342 -- Connecting to existing Ray cluster at address: 10.0.0.77:6379...
2022-12-29 10:35:57,764 INFO worker.py:1528 -- Connected to Ray cluster.
Setting up ASE
Starting optimization
Step Time Energy fmax
BFGS: 0 10:36:02 -68517.913397 3.5472
BFGS: 1 10:36:04 -68519.616345 2.8398
BFGS: 2 10:36:05 -68524.450556 2.0596
BFGS: 3 10:36:06 -68527.262168 3.1269
BFGS: 4 10:36:07 -68528.911255 2.3024
BFGS: 5 10:36:09 -68530.098907 1.8428
BFGS: 6 10:36:10 -68531.107443 2.6093
BFGS: 7 10:36:11 -68531.888864 2.6436
BFGS: 8 10:36:12 -68532.375126 1.6772
BFGS: 9 10:36:13 -68532.730120 1.7315
BFGS: 10 10:36:15 -68533.327400 1.0089
BFGS: 11 10:36:16 -68533.879248 1.3293
BFGS: 12 10:36:17 -68534.276709 1.6804
BFGS: 13 10:36:18 -68535.285333 1.4898
BFGS: 14 10:36:19 -68535.773468 1.1612
BFGS: 15 10:36:21 -68535.897528 1.2659
BFGS: 16 10:36:22 -68536.193563 1.0326
BFGS: 17 10:36:23 -68536.543744 0.7357
BFGS: 18 10:36:25 -68536.814560 1.3871
BFGS: 19 10:36:26 -68536.971200 1.0031
BFGS: 20 10:36:27 -68537.250519 1.1595
BFGS: 21 10:36:28 -68537.372511 1.2645
BFGS: 22 10:36:30 -68537.546845 1.1778
BFGS: 23 10:36:31 -68537.783378 1.8484
BFGS: 24 10:36:32 -68537.889268 2.0116
BFGS: 25 10:36:33 -68538.134710 0.8240
BFGS: 26 10:36:34 -68538.277066 0.7056
BFGS: 27 10:36:35 -68538.500159 0.9197
BFGS: 28 10:36:37 -68538.676092 1.2324
BFGS: 29 10:36:38 -68538.859638 0.8854
BFGS: 30 10:36:39 -68539.012425 0.5784
BFGS: 31 10:36:40 -68539.016547 0.6297
BFGS: 32 10:36:41 -68539.186143 0.6434
BFGS: 33 10:36:42 -68539.331553 0.4745
BFGS: 34 10:36:43 -68539.453231 0.9449
BFGS: 35 10:36:45 -68539.600969 0.8556
BFGS: 36 10:36:46 -68539.771981 0.8342
BFGS: 37 10:36:47 -68539.845176 0.7681
BFGS: 38 10:36:48 -68539.969053 0.5224
BFGS: 39 10:36:49 -68540.155790 0.6128
BFGS: 40 10:36:50 -68540.380225 0.6529
BFGS: 41 10:36:52 -68540.319302 0.5663
BFGS: 42 10:36:53 -68540.382694 0.7651
BFGS: 43 10:36:54 -68540.440462 0.7541
BFGS: 44 10:36:55 -68540.540893 0.8772
BFGS: 45 10:36:56 -68540.642185 0.4752
BFGS: 46 10:36:57 -68540.714986 1.2217
BFGS: 47 10:36:59 -68540.785903 0.9823
BFGS: 48 10:37:00 -68540.776744 0.7590
BFGS: 49 10:37:01 -68540.783109 0.6044
BFGS: 50 10:37:02 -68540.871331 0.4871
BFGS: 51 10:37:03 -68540.987260 0.5234
BFGS: 52 10:37:04 -68541.096528 0.6751
BFGS: 53 10:37:06 -68541.161885 0.6271
BFGS: 54 10:37:07 -68541.188346 0.5450
BFGS: 55 10:37:08 -68541.255231 0.6397
BFGS: 56 10:37:09 -68541.221991 0.4792
BFGS: 57 10:37:10 -68541.295788 0.4745
BFGS: 58 10:37:11 -68541.352476 0.5650
BFGS: 59 10:37:13 -68541.431386 0.5724
BFGS: 60 10:37:14 -68541.262401 0.7457
BFGS: 61 10:37:15 -68541.452363 0.6275
BFGS: 62 10:37:16 -68541.518779 0.4439
BFGS: 63 10:37:17 -68541.568480 0.3567
Writing XYZ file
Done!
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