glp turns any graph-based machine-learning potential implemented in jax into a jit-able calculator ready for molecular dynamics. It provides unified implementations of forces, stress, and (with caveats) the heat flux.
In a nutshell: If you provide a function that maps a Graph of atom-pair vectors to atomic potential energies, glp takes care of everything else. ✨
With glp, we aim to make it straightforward to go from implementing a new machine-learning potential to using it for moderate-sized production runs (thousands of atoms, nanoseconds of MD). glp also serves as an illustration of implementations of stress with automatic differentiation. It was written to support the following paper:
Stress and heat flux via automatic differentiation
by Marcel F. Langer, J. Thorben Frank, and Florian Knoop
J. Chem. Phys. 159, 174105 (2023)
Preprint: arxiv:2305.01401 (2023)
If you use this code in an academic context, please cite this preprint. If you use the heat flux, please also cite this other paper. 🙏
glp is considered essentially "finished" -- expect mostly occasional maintanance updates. Feel free to file issues if things break.
See also: gkx, which implements the remaining parts for a fully jax-based Green-Kubo workflow.
Once you supply a Potential with the required interface (see below), glp gives you:
aseCalculatorwithFHI-vibesintegration that can compute energy, forces, stress, and heat fluxjit-ready calculation functions as building blocks for more advanced workflows for energy, forces, stress and heat flux- Full support for periodic systems, including those with non-orthorhombic cells, and including any changes of those cells
- Velocity verlet integrator ready for
lax.scan(mostly for fun, but fast nevertheless)
To our knowledge, it is the first tool that implements the heat flux, required for the calculation of thermal conductivity with the Green-Kubo method, for autodiff-based machine-learning potentials.
If you don't want to implement a potential, we also have a direct interface with mlff that implements the state-of-the-art so3krates MLP.
Apart from these more "user-facing" features, glp also
- takes care of all the logic required to pad and invalidate neighborlists, even if the simulation cell changes.
- provides a simple interface for taking care of
jit-ing dynamics simulations where inputs can change. - demonstrates how to implement forces, stress, and heat flux in different ways with automatic differentiation.
- is extensively tested for correctness of the implementation of these quantities.
glp currently can't do the following:
- Support training of MLPs (even though it could be pressed into service with some hacking)
- Support truly non-local MLPs (forces will likely work, but don't really require the whole machinery of
glp) - Scale to very large systems, because the neighbourlist is implemented naively and scales quadratically with system size. It's fine for serious runs with up to a few thousand atoms.
- Take care of full MD workflows: we don't do the simulation (except, experimentally, NVE) and we don't take care of the surrounding logic of logging, i/o, etc.
A Potential is a function that maps a Graph to an ndarray of atomic potential energies.
It is declared in glp as:
from glp import Potential
potential = Potential(potential_fn, cutoff)For forces and stress, this represents all glp needs to know about your potential. For heat flux, you additionally need to supply an effective_cutoff that quantifies the maximum range of interactions beyond local environments, for instance through message-passing (where it is n_interactions * cutoff).
A Potential currently can't carry internal state, and is not expected to have non-local interactions; we basically expect either a potential that works within neighbourhoods or with message passing.
The input data structure for a Potential is
Graph = namedtuple("Graph", ("edges", "nodes", "centers", "others", "mask"))We adopt the "sparse" convention of jax-md, where we store flat ndarrays of pairs n_pairs rather than the more old-school "dense" format where we store n_atoms x n_neighbors.
Then:
edgesare atom-pair vectorsr_ij = r_j - r_i(with the minimum image convention applied)nodesare atomic numbers (may be used for different node labels in the future)centersare indices indicating whichibelongs to which entry inedgesothersare corresponding indicesjmaskis a boolean array indicating which entries inedgesare padding (indices for these are set ton_atoms)
For an example, you may want to check the lennard_jones potential.
The real heart of glp are the calculators, which are the functions that actually make use of a Potential to compute quantities of interest. Due to the constraints of jax, they are a bit more complicated than one would maybe expect: They have to balance the need for being jit-able, which needs static input/output shapes, with the fact that the system can change unpredictably during simulation.
Luckily, we already did all of the work and you can just use the ready-made calculators! Nevertheless, to use them, you need to understand how they work a bit.
Our solution to this jit problem is to carry around a state, which is some namedtuple (or more generally any pytree) that carries around all the runtime information needed between steps. It can be updated within the jit at every step, and it can yield an overflow when changes have accumulated that can't be dealt with in a jit-able way. If an overflow occurs, we basically create the calculator again and get a new state to start from. Overflows are indicated by state.overflow == True. If this occurs, the results returned by the calculator are wrong and must be discarded! (For those familiar with jax-md, this is essentially how their NeighborList operates -- we just extend this slightly to support other transformations.)
A Calculator is therefore defined as two functions:
Calculator = namedtuple("Calculator", ("calculate", "update"))calculate is a jit-able function from System, state (System is defined below) to results, state. update takes only a System and returns a new Calculator and a new state.
The calculator functions implemented in glp currently (for an overview see the readme in glp/calculators) all have the following interface:
from glp.calculators.some_calculator import calculator
my_calculator = calculator(
system, # example of the system we want to investigate
potential, # instance of Potential
skin=0.1, # additional cutoff used for caching the neighborlist
capacity_multiplier=1.25, # add 25% more pairs to neighborlist as spare capacity
**kwargs, # additional arguments
)It's often inconvenient to keep track of all the arguments, so in some places, a get_calculator function is used that is simply a partial of calculator that fixes all arguments except system. The .update function is basically the same thing: it takes a system and returns a Calulator, state tuple.
An overview of available calculators is given in here. In general, we recommend:
atom_pairfor energy, forces, stress (equivalent toend_to_end)atom_pairwithheat_flux=Truefor heat flux for models without message passing. It will produce wrong results for models with message passing.heat_flux_unfoldedfor heat flux for models with message passing. This calculator constructs an extended "unfolded" simulation cell (see this preprint) and therefore is slower and needs more memory than others.supercellfor energy, forces, stress in the case where simulation cells are smaller than the cutoff of the potential (for instance, relaxing primitive cells)
Other calculators exist to illustrate different approaches but are not typically needed for production use.
The System is the internal representation of an arrangement of atoms:
System = namedtuple("System", ("R", "Z", "cell"))Where R are the positions, Z atomic numbers, and cell either lattice vectors (each vector a column) or None (for molecules).
You will likely not have to instantiate this by hand, glp provides an atoms_to_system() method that turns an ase.Atoms into a System.
If you already have a mlff model or want to test things with a Lennard-Jones potential, you can make use of the glp.instantiate module, which implements a convenience interface to create the various things defined by glp from specable-style dictionaries.
It works like this:
from glp import instantiate
potential_dict = {"mlff": {"folder": "path/to/model"}}
potential_dict = {"lennard_jones": {"sigma": 3.405, "epsilon": 0.01042, "cutoff": 10.5, "onset": 9.0}}
# get a get_calculator function with a given potential and calculator
get_calculator = instantiate.get_calculator(potential_dict, {"atom_pair": {"skin": 0.1}})
# ... just for jax:
calculator, state = get_calculator(system)
# ... or for ase/vibes:
from glp.ase import Calculator
calculator = Calculator(get_calculator)For FHI-vibes, you can also use:
[calculator]
name: calculator
module: glp.vibes
[calculator.parameters.calculator]
calculator: atom_pair
skin: 0.1
[calculator.parameters.potential]
potential: lennard_jones
sigma: 3.405
# ...
First, you need to make sure to have a working jax installation. Then:
git clone git@github.com:sirmarcel/glp.git
cd glp
# minimal install
pip install .
The ase, mlff, and vibes interfaces require these libraries to be installed.
For ase and vibes, you can let pip do this for you:
# for everything (vibes, ase)
pip install ".[full]"
# or...
pip install ".[vibes]"
pip install ".[ase]"
Currently, for some reason, mlff must be installed manually by running
git clone git@github.com:thorben-frank/mlff.git
cd mlff
pip install -e .
glp is essentially unit agnostic, it simply manipulates numbers as given. The dynamics module assumes everything is in ase units, so the timestep is in ase.units.fs. For compatibility with ase, it is best to stick to Ångstrom for distances and eV for energies.
Stress and heat flux are internally computed without dividing by the volume, but the standard convention is enforced in the ase calculator, where we also convert the heat flux to being in SI-ps instead of ase-fs, in line with the FHI-vibes conventions. To circumenvent all such processing, the raw=True argument can be passed.
Much of the original design of glp was heavily inspired by jax-md. Since then, we've decided to take some slightly different technical directions, which allow us to take a more direct approach to treating periodic systems and the associated tasks of computing the stress.
In jax-md, potentials are typically defined via their parameters and a displacement_fn (computing minimum image convention atom-pair vectors) that encodes the simulation cell. This means that the cell is a parameter, rather than a direct argument of the potential energy function, so taking derivatives with respect to the cell or computing the stress is a bit awkward (but possible). It also means that the potential is responsible for mapping the displacement_fn over pairs of neighbours, typically with the help of a neighborlist. At the time of writing, jax-md also implements the displacement in general periodic systems such that the derivative with respect to the cell is incorrect, so the stress must be computed by transforming the displacements.
In contrast, glp takes the perspective that potentials are strictly functions mapping (positions, charges, cell) to a potential energy. It provides tools to easily implement a particular class of such general potentials: Those that internally represent (positions, charges, cell) as a graph of minimum-image convention atom-pair vectors between nodes (atoms) labeled with charges. We take care of constructing this graph and therefore take charge of dealing with displacement functions and neighborlists, which are no longer the responsibility of a given potential.
This means that the function signatures involved cleanly represent that underlying concepts, and so we don't need to jump through any hoops to obtain the stress with AD -- with whatever implementation we'd like, even those that directly transform positions and cell.
In any case, it should be fairly straightforward to adopt jax_md.energy functions for glp, if desired, and we are looking forward to PRs in that direction!
Please also see the technical documentation of glp in the glp folder. Otherwise, just read the code! It's probably about the same number of lines as this readme.
For glp, the next steps are outlined in the technical readme: there is some work to be done to scale to larger systems.
In a larger context, glp aims to be a neat building block for larger systems. In particular, we're planning to use it as one part of a future molecular dynamics package, the seeds of which you can find in glp/dynamics and mlff/mdx. However, we're still gathering some experience on how these tools work in practice, and are thinking about the correct abstractions to build this thing.