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AtomsBase Interface

ACEpotentials has a new AtomsBase based interface in addition to JuLIP based interface.

AtomsBase allows easy communication between different Julia programs. In the future this interface will became the default one and JuLIP interface will be retired.

AtomsBase interface has not been rigorously tested yet. So, expect some issues here and there. But you are recommended to git it a try.

Loading Training Data

With AtomsBase you can use AtomsIO to load training data

using AtomsIO

data = load_trajectory("path to training data")

You can also use ExtXYZ directly (exported by ACEpotentials) to load training data

data = ExtXYZ.load("path to training data")

To use AtomsBase with the examples you can load the training data in AtomsBase format by giving a keyword argument atoms_base=true

data, _, meta = ACEpotentials.example_dataset("TiAl_tutorial"; atoms_base=true)

Training with AtomsBase

There are no changes to the training methods when using AtomsBase. You only need to have the training data in AtomsBase format for the training to work. Here is the acemodel style training tutorial using AtomsBase

using ACEpotentials


data, _, meta = ACEpotentials.example_dataset("TiAl_tutorial"; atoms_base=true)

model = acemodel(
    elements = [:Ti, :Al],
	order = 3,
	totaldegree = 6,
	rcut = 5.5,
	Eref = [:Ti => -1586.0195, :Al => -105.5954]
)
@show length(model.basis);


weights = Dict(
    "FLD_TiAl" => Dict("E" => 60.0, "F" => 1.0 , "V" => 1.0 ),
    "TiAl_T5000" => Dict("E" => 5.0, "F" => 1.0 , "V" => 1.0 )
);

solver = ACEfit.LSQR(damp = 1e-2, atol = 1e-6);
data_train = data[1:5:end]
P = smoothness_prior(model; p = 4) 

acefit!(model, data_train; solver=solver, weights=weights, prior = P);

@info("Training Error Table")
ACEpotentials.linear_errors(data_train, model; weights=weights);

Training data in AtomsBase structures

In AtomsBase you have system wide features accesses with haskey(some_key) or atom features accesses with hasatomkey(some_key). Energy (scalar) and virial (matrix) are expected to be system features while force (vector) should be a atom feature. They should be unitless. The fitting process does not have internal units. But in the data the units are implicitely expected to be in eV and eV/Å, when units are stripped.

By default all these should be true

haskey(system, :energy)     # default energy key
haskey(system, :virial)     # default virial key
hasatomkey(system, :force)  # default force key

Weights with AtomsBase

With AtomsBase weights are stored in AtomsBase structures and there is no need to create AtomsData structures. Weights can be given for either energy, forces or virial and for structure itself. Each of these have an associated keyword

  • :energy_weight for energy
  • :force_weight for forces
  • virial_weight for virial
  • :weight a general weight for the structure that multiply other weights

To access the weights you can call

data_point[:energy_weight]
data_point[:force_weight]
data_point[:virial_weight] 
data_point[:weight]

To set a weight by hand on an individual structure you can use

# Set general weight
data_point[:weight] = 60
## AtomsCalculators support
# Set weight for energy
data_point[:energy_weight] = 60

# etc.

When you use acemodel interface (call acefit!) the weights are applied by overwriting any existing weights.

You can look for what keys AtomsBase structures support by calling

# whole structure features
keys(data_point)

# features per atom
atomkeys(data_point)

You can give keyword group_key to acefit! to determine what group weights are used. Make sure that corresponding haskey call returns true.

New Assemble Backend

AtomsBase interface uses new assemble backend that is faster than the old one. You can you the new backend with old JuLIP interface by giving keyword new_assembly=true. E.g.

# acefit interface
acefit!(model, data_train; solver=solver, weights=weights, prior = P, new_assembly=true);

# acebasis interface
ACEfit.assemble(data_train, basis; new_assembly=true)

You can control what keys are used for energy, forces and virial by using keyword arguments energy_key, force_key and virial_key. Look for document sting for more details and more contron options.

AtomsCalculators Interface

To use AtomsBase structures as an input for calculations you need to create ACEpotential structure. If you use acemodel interface (like above) you can do this with

pot = ACEpotential(model)

If you use acebasis interface you can create potential with

pot_1 = ACEpotential(basis, results["C"])

Alternatively you can load the potential from a file

pot = load_potential("my-potential.json"; new_format=true)

ACEpotential stucture implements AtomsCalculators interface

using AtomsCalculators

E = AtomsCalculators.potential_energy(system, pot)
F = AtomsCalculators.forces(system, pot)
V = AtomsCalculators.virial(system, pot)

where system is an AtomsBase structure.

The current ACE1 based implemetation to AtomsBase and AtomsCalculators is implemented in ACEmd. Take a look onto it, if you need further information.