M3GNet: Universal ML Potential

Note: This tutorial requires AMS2023 or later.

This tutorial will teach you how to:

• Download and install the M3GNet-UP-2022 machine learning (ML) potential 1 for the entire periodic table, especially suitable for organic and inorganic crystal materials. M3GNet-UP-2022 was fitted to PBE reference data.

• Use the D3 Dispersion Engine Addon to add Grimme’s D3 dispersion to the energy, forces, and stress tensors.

• Calculate the cohesive energy of the molecular naphthalene crystal.

See also

• MLPotential documentation

• Machine Learning Thermochemistry

• Crystals and Surfaces

Note

M3GNet can also be applied to inorganic crystals like metals and metal oxides.

Install M3GNet

First, make sure to install the M3GNet package inside AMS.

Open the package manager: SCM → Packages

M3GNet runs much faster on a GPU than a CPU. If you have a CUDA-enabled GPU on your machine:

Click the ML options button on the top right

Select the CPU or CUDA version (if you’re unsure, select mlcpu)

Click confirm

Then, download and install M3GNet:

Select M3GNet

Click Install, if it’s not already installed

Wait for the download and installation to complete. It may take a while!

Cohesive energy

To calculate the cohesive energy of solid naphthalene, you need to calculate the energy of

• a single naphthalene molecule in the gasphase

• the naphthalene crystal

The naphthalene crystal unit cell contains two naphthalene molecules, so ultimately we want to calculate the reaction energy

\[E_{\textrm{coh}} = \frac{ 2 E_{\textrm{gas}} - E_{\textrm{crystal}} }{2}\]

Gasphase naphthalene

Open AMSinput: SCM → New input

Switch to ML potential: →

Set the Task to Geometry Optimization

Set the Model to M3GNet-UP-2022 (UP = Universal Potential)

File → Import system and select naphthalene_gas.xyz

To add D3(BJ) dispersion corrections:

Go to Details → Expert AMS

Under EngineAddons D3Dispersion, set Enabled → Yes

If you have a CUDA-enabled GPU, then you can go to the Details → Technical panel and set Device to cuda:0. However, for a small system like naphthalene, running on a GPU does not provide significant speedup (in practice, the D3 dispersion calculation is about as computationally expensive as the M3GNet calculation).

Then save and run the job:

1. Select File → Save and name it, e.g., naphthalene_gas.ams

2. Click on File → Run

Crystalline naphthalene

Set up crystalline naphthalene exactly as the gasphase calculation, with two exceptions:

Import naphthalene_crystal.xyz instead

On the Details → GeometryOptimization panel, set Optimize lattice → Yes.

Make sure the D3Dispersion is set as before

Some of the molecules cross the periodic boundaries, so that the atoms in the same molecule are shown on different sides of the unit cell. This can be confusing. AMSinput offers two ways to make the visualization easier:

Set View → Periodic → Periodic View Type → View Outside

Set View → Periodic → Periodic View

This shows some periodic replicas of atoms that are “just outside” the unit cell, but does not change any atomic positions.

Alternatively, you can move the atoms so that all molecules are shown intact (thus placing some atoms outside the unit cell):

Set Edit → Crystal → Map Molecules Complete

It is up to you if you prefer to have the molecules split across the unit cell or not. It makes no difference to the calculation.

Now save with a new name and run the job:

1. Select File → Save and name it, e.g., naphthalene_crystal.ams

2. Click on File → Run

Lattice optimization results

The easiest way to get the optimized lattice parameters is to generate a spreadsheet report:

Select the finished job in AMSjobs

Tools → Build Spreadsheet…

The optimized cell lengths and angles are shown on the left-hand side.

You can also view the optimized structure in AMSmovie.

Calculate cohesive energy

Collect the energies from the gasphase and crystal calculations, either from a spreadsheet as above or by scrolling down towards the end of the .out file (SCM → Output).

See also

10 Ways to Get the Energy and Other Properties

You should get E_gas = -4.41213477 Ha and E_crystal = -8.89238031 Ha, giving E_coh = 0.03406 Ha = 89 kJ/mol.

This compares well to PBE-TS numbers (TS is a different type of dispersion correction) reported by Al-Saidi et al 2:

property	PBE-TS 2	M3GNet-D3(BJ)
Ecoh (kJ/mol)	95	89
a (Å)	8.01	7.99
b (Å)	5.90	6.02
c (Å)	8.62	8.59

Tip

M3GNet is also suitable for inorganic crystals like metals and metal oxides.

M3GNet in Python with PLAMS

See the M3GNet example in the PLAMS documentation.

References

1

C. Chen, S. P. Ong. Nature Computational Science 2, 718–728 (2022). arXiv.2202.02450.

2(1,2)

W.A. Al-Saidi, V.K. Voora, K.D. Joradan. DOI: 10.1021/ct200618b