[ase-users] Save SocketIOCalculator property to file

[Offermans Willem]

Dear ASE friends,

I dug into the code.

The class TrajectoryReader in io/trajectory.py has a method called __getitem__.

If I understand it correctly it will set the calculator to SinglePointCalculator upon reading
a trajectory file. Is my understanding correct? Does this mean we cannot save calculator
objects, other than SinglePointCalculator, together with atoms objects to a file?


    def __getitem__(self, i=-1):
        b = self.backend[i]
        if 'numbers' in b:
            # numbers and other header info was written alongside the image:
            atoms = read_atoms(b)
        else:
            # header info was not written because they are the same:
            atoms = read_atoms(b, header=[self.pbc, self.numbers, self.masses,
                                          self.constraints])
        if 'calculator' in b:
            results = {}
            implemented_properties = []
            c = b.calculator
            for prop in all_properties:
                if prop in c:
                    results[prop] = c.get(prop)
                    implemented_properties.append(prop)
            calc = SinglePointCalculator(atoms, **results)
            calc.name = b.calculator.name
            calc.implemented_properties = implemented_properties

            if 'parameters' in c:
                calc.parameters.update(c.parameters)
            atoms.set_calculator(calc)

        return atoms



Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 20 Jan 2020, at 16:17, Offermans Willem via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Dear ASE friends,

If I save atoms objects to a file, the attached calculator object get lost.

I read a trajectory file with atoms objects. The calculators of each are
set to ``calculator=SinglePointCalculator(…)``. If I change this to
``calculator=SocketIOCalculator(…)`` and save the atoms objects to
a file, the calculator is reset upon next read.

Most probably, the info about the calculator is not saved and the settings of
``calculator=SinglePointCalculator(…)`` is initialised during read.
Is this correct?

Is it possible to save the calculator to a file as is done when saving the atoms
object to a database?
How can I save the calculator setting?




Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>

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