ASE Calculator for AMS

Introduction

The AMSCalculator class is an ASE Calculator that lets you use any AMS engine (ADF, BAND, DFTB, ReaxFF, MLPotential, ForceField, …) together with ASE.

See also

Example: AMSCalculator: ASE geometry optimizer with AMS forces

Engine ASE: Couple external ASE calculators to the AMS Driver

Technical

Before using an AMSCalculator, you must call the init() function from PLAMS. This is done automatically if you use the plams binary.

AMS settings

A Settings object is used to set up the AMS settings in the same way as for normal PLAMS jobs.

See also

Preparing input for AMS jobs in PLAMS

ASE results

Currently only the energy, forces and stress tensor are provided through the ASE interface. All other results can be accessed through AMSCalculator.ams_results, which is an AMSResults object. Use AMSCalculator.ensure_property('forces') and AMSCalculator.ensure_property('stress') to ensure these ASE properties are computed regardless of whether it was originally requested in the Settings object.

Charge

There is currently no universal interface in ASE for the total charge of a system and is instead considered to be Calculator specific. The easiest way to set the charge a calculation with the AMSCalculator is to define Atoms.info['charge']. Additionally, when the charge needs to be treated extensively w.r.t. manipulations of the Atoms object in ASE, the initial charge of each atom can also be set. The total charge is thus obtained as sum(Atoms.get_initial_charges())+Atoms.info['charge']. See the ASE documentation for details on initial charges and info.

See also

Example: AMSCalculator: Access results files & Charged systems

AMS standalone and worker mode

AMS can run in two modes: standalone and worker.

In standalone mode (amsworker=False), AMS is started for every new structure, and stores the normal AMS output. Use this mode if:

• you need to access all results, or

• you run a calculation not supported by the AMSworker (e.g., a PESScan)

In AMSworker mode (amsworker=True), AMS is only started once. This significantly reduces overhead, especially for fast engines like ReaxFF. The downside is that you cannot access all results. Use this mode if:

• you only need access to energy, forces, and stress tensor, and

• you only need to run single point calculations, for example to use the ase.optimize.BFGS geometry optimizer.

Technical

In AMSworker mode, make sure to use AMSCalculator as a context manager, or explicitly call AMSCalculator.stop_worker() when you want to terminate the AMS process.

Technical

Technical

When creating a deepcopy of AMSCalculator the AMSWorker is not copied and instead every copy of AMSCalculator has a reference to the same AMSWorker.

AMSCalculator API

class AMSCalculator(settings=None, name='', amsworker=False, restart=True, molecule=None, extractors=[])

ASE Calculator which can run any AMS engine (ADF, BAND, DFTB, ReaxFF, MLPotential, ForceField, …).

The settings are specified with a PLAMS Settings object in the same way as when running AMS through PLAMS.

Technical

Before initializing the AMSCalculator you need to call plams.init():

from scm.plams import *
init()

Parameters:

settingsSettings

A Settings object representing the input for an AMSJob or AMSWorker. This also determines which implemented_properties are available: settings.input.ams.properties.gradients: force settings.input.ams.properties.stresstensor: stress

namestr, optional

Name of the rundir of calculations done by this calculator. A counter is appended to the name for every calculation.

amsworkerbool , optional

If True, use the AMSWorker to set up an interactive session. The AMSWorker will spawn a seperate process (an amsdriver). In order to make sure this process is closed, either use AMSCalculator as a context manager or ensure that AMSCalculator.stop_worker() is called before python is finished:

with AMSCalculator(settings=settings, amsworker=True) as calc:
    atoms.set_calculator(calc)
    atoms.get_potential_energy()

If False, use AMSJob to set up an io session (a normal AMS calculation storing all output on disk).

restartbool , optional

Allow the engine to restart based on previous calculations.

moleculeMolecule , optional

A Molecule object for which the calculation has to be performed. If settings.input.ams.system is defined it overrides the molecule argument. If AMSCalculator.calculate(atoms = atoms) is called with an atoms argument it overrides any earlier definition of the system and remembers it.

extractors: List[BasePropertyExtractor] , optional

Define extractors for additional properties.

Examples:

static __new__(cls, settings=None, name='', amsworker=False, restart=True, molecule=None, extractors=[])

Dispatch object creation to AMSPipeCalculator or AMSJobCalculator depending on AMSWorker

property implemented_properties

Returns the list of properties that this calculator has implemented

calculate(atoms=None, properties=['energy'], system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])

Calculate the requested properties. If atoms is not set, it will reuse the last known Atoms object.

ensure_property(properties)

A list of ASE properties that the calculator will ensure are available from AMS or it gives an error.

stop_worker()

Stops the amsworker if it exists

clean_exit()

Function called by ASEPipeWorker to tell the Calculator to stop and clean up