150 ps NVT · UMA-s-1.2.1 and DPA4C-Plus

Dy versus Nd: how many hydroxides stay on the metal

With DPA4C-Plus, Dy keeps more hydroxide in the first shell than Nd under every boundary condition. Averaged with equal weight over the four boundaries and five temperatures, the bound-hydroxide count is 2.37 for Dy and 1.75 for Nd. Each number is one 150 ps trajectory.

With UMA-s-1.2.1 the two metals both stay near three hydroxides in the open box and in both droplets. In the periodic box they do not. Nd remains at three (3.00, 3.00, 3.00, 2.99, 3.00 from 300 to 500 K). Dy does not (0.37, 0.03, 1.01, 2.11, 0.15). Those five Dy runs are separate trajectories, and they do not share one outcome: the hydroxide leaves, a bare oxygen stays inside 3.0 Å, or two hydroxides remain.

Raw trajectories

All 240 trajectories are on NERSC Perlmutter, readable by every NERSC user (read-only):

cd /global/cfs/cdirs/m4517/jiaao/genesis/md/ln-150ps/runs

Layout <model>/<boundary>/<metal>/T<K>/, for example uma-s-1.2.1/box_pbc/Nd/T300/. Model is uma-s-1.2.1 or DPA4C-Plus. Boundary is box_pbc, box_nonpbc, droplet_pbc or droplet_nonpbc. Each folder holds traj.extxyz (frames every 0.1 ps with positions, momenta, forces and energy; about 90 MB), md.log, checkpoint.extxyz (last frame) and done.json. The folders also contain Er, Gd, La and Lu runs that are not shown on this page.

Initial structure (interactive)

Representative metal: Nd (spin multiplicity 4). Composition Nd³⁺ + 3 OH⁻ + 128 H₂O, 391 atoms, charge 0. Drag to rotate, scroll to zoom. The four buttons switch the boundary-condition geometry used in the MD set.

Nd O H

Nd · box, periodic · drag to rotate

Distance of the three t = 0 hydroxide oxygens

The three traces are the three oxygens that are hydroxide at 0 ps (at most one H within 1.20 Å). Each frame they are reordered into nearest, middle and farthest. Left column, Nd. Right column, Dy. The dashed line is 3.10 Å and the dotted line is 5 Å. A red mark is the first time fewer than three of those oxygens remain inside 3.10 Å. This is the same definition as plot_oh_distance_Dy_vs_Nd.py in the plot-scripts-v1 release.

uma_distance at 300 K, four boundary conditions, Nd and Dy

UMA turbo versus UMA default at 300 K

Left column: the previous production, UMA-s-1.2.1 turbo, friction 1 ps⁻¹. Right column: the run that uses the v2026-09-04 input settings, UMA-s-1.2.1 default (TF32 off), friction 0.01. Both are one 150 ps trajectory at 300 K from the same starting geometry. The three traces, the 3.10 Å and 5 Å lines, and the leave mark use the same definition as the distance figure above. Green, nearest. Orange, middle. Blue, farthest.

Nd, 300 K, UMA turbo on the left and UMA default on the right, four boundary conditions

Leave is the first time fewer than three of the t = 0 hydroxide oxygens remain inside 3.10 Å. “stays” means that did not happen in 150 ps. Farthest is the maximum of the blue trace, in Å. Each row is one trajectory.

Metal	Boundary	turbo leave	default leave	turbo farthest / Å	default farthest / Å
La	Box, periodic	47.4 ps	83.4 ps	8.56	3.43
La	Box, non-periodic	24.7 ps	75.2 ps	8.07	3.18
La	Droplet, periodic	31.1 ps	85.3 ps	8.05	14.15
La	Droplet, non-periodic	7.6 ps	16.3 ps	3.31	3.43
Nd	Box, periodic	stays	33.5 ps	2.67	5.97
Nd	Box, non-periodic	97.4 ps	55.2 ps	3.21	13.39
Nd	Droplet, periodic	23.1 ps	stays	3.63	2.87
Nd	Droplet, non-periodic	18.2 ps	56.1 ps	3.39	11.71
Gd	Box, periodic	0.5 ps	0.3 ps	3.99	5.61
Gd	Box, non-periodic	stays	52.5 ps	2.85	4.79
Gd	Droplet, periodic	stays	0.1 ps	2.99	11.78
Gd	Droplet, non-periodic	110.9 ps	0.2 ps	10.68	11.29
Dy	Box, periodic	1.2 ps	2.5 ps	5.22	4.68
Dy	Box, non-periodic	36.9 ps	65.9 ps	4.41	10.78
Dy	Droplet, periodic	134.8 ps	28.4 ps	3.39	8.42
Dy	Droplet, non-periodic	129.8 ps	stays	3.28	2.80
Er	Box, periodic	stays	stays	2.49	2.50
Er	Box, non-periodic	stays	stays	2.69	2.71
Er	Droplet, periodic	70.3 ps	stays	10.44	2.98
Er	Droplet, non-periodic	stays	stays	2.83	2.50
Lu	Box, periodic	stays	stays	2.70	2.47
Lu	Box, non-periodic	stays	stays	2.43	2.52
Lu	Droplet, periodic	stays	stays	2.48	2.80
Lu	Droplet, non-periodic	stays	stays	2.46	2.47

Time average of the bound-hydroxide count

UMA-s-1.2.1. Each entry is the 0–150 ps mean of one trajectory. The cutoff is 3.0 Å.

Boundary	Metal	300 K	350 K	400 K	450 K	500 K	Mean
Box, periodic	Nd	3.00	3.00	3.00	2.99	3.00	3.00
Box, periodic	Dy	0.37	0.03	1.01	2.11	0.15	0.73
Box, non-periodic	Nd	2.91	2.91	2.94	2.99	3.00	2.95
Box, non-periodic	Dy	2.88	2.99	2.97	2.99	3.00	2.97
Droplet, periodic	Nd	2.73	2.98	2.90	2.95	2.96	2.90
Droplet, periodic	Dy	2.79	2.93	2.93	2.96	2.99	2.92
Droplet, non-periodic	Nd	2.98	2.94	2.87	2.98	3.00	2.95
Droplet, non-periodic	Dy	2.78	2.95	2.96	2.99	3.00	2.94

DPA4C-Plus.

Boundary	Metal	300 K	350 K	400 K	450 K	500 K	Mean
Box, periodic	Nd	0.62	0.47	1.46	1.39	2.14	1.21
Box, periodic	Dy	1.16	2.02	2.21	2.53	2.65	2.12
Box, non-periodic	Nd	0.78	1.63	2.09	2.53	2.81	1.97
Box, non-periodic	Dy	2.22	1.69	2.58	2.86	2.97	2.47
Droplet, periodic	Nd	1.05	1.47	1.89	2.73	2.84	2.00
Droplet, periodic	Dy	1.43	2.22	2.51	2.92	2.87	2.39
Droplet, non-periodic	Nd	0.64	1.18	1.80	2.68	2.75	1.81
Droplet, non-periodic	Dy	2.58	2.05	2.27	2.78	2.89	2.51

Simulation

Composition Ln³⁺ + 3 OH⁻ + 128 H₂O, 391 atoms, charge 0. Nd spin multiplicity 4. Dy spin multiplicity 6.
UMA-s-1.2.1 from uma-s-1p2p1.pt, fairchem turbo, task omol, TF32. Spin is written as the multiplicity on every energy and force call.
DPA4C-Plus from frozen.pt2, charge_spin = [0, multiplicity], TF32 inference. The checkpoint default [0, 1] is not used.
NVT Langevin, 1 fs, 150 ps, friction 1 ps⁻¹, fixed cell. Frames every 0.1 ps. Temperatures 300, 350, 400, 450 and 500 K, one trajectory each.
Box length 15.782 Å. Droplet periodic cell 42.218 Å.