[ase-users] Questions regarding the calculate() method

[Ask Hjorth Larsen]

Dear Ivan,

2018-01-16 15:13 GMT+01:00 Kondov, Ivan (SCC) via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Dear all,
>
> I want to do a geometry optimization and get back the optimized structure,
> the energy and the forces. Here is an example:
>
> from ase.build import molecule
> from ase.calculators.nwchem import NWChem
> atoms = molecule('NH3')
> calc = NWChem(task='optimize', xc='pbe0')
> atoms.set_calculator(calc)
> print(atoms.get_positions())
> calc.calculate(atoms)
> print(print(atoms.get_potential_energy()))
> print(atoms.get_positions())
> print(atoms.get_forces())
>
> [[ 0.        0.        0.116489]
>  [ 0.        0.939731 -0.271808]
>  [ 0.813831 -0.469865 -0.271808]
>  [-0.813831 -0.469865 -0.271808]]
> -1528.1988692333646
> [[ 0.        0.        0.116489]
>  [ 0.        0.939731 -0.271808]
>  [ 0.813831 -0.469865 -0.271808]
>  [-0.813831 -0.469865 -0.271808]]
> [[ -1.02844134e-04   1.54266201e-04  -2.41683715e-03]
>  [  5.14220671e-05   1.54266201e-04   8.22753073e-04]
>  [  3.08532403e-04  -1.54266201e-04   7.71331006e-04]
>  [ -2.05688268e-04  -1.54266201e-04   8.22753073e-04]]
>
> The energy and the forces are correct but not the structure (it should be
> updated).
>
> 1) The reason for this behavior is that Calculator.calculate()  works on a
> copy of the atoms object if it has been supplied as argument:
>
> if atoms is not None:
>     self.atoms = atoms.copy()
>
> Is this the wished behavior? Because the only way to get to the updated
> atoms object is then using this detour: calc.atoms.get_positions() in the
> user function.
>
> 2) Then the solution would be to simply not specify the atoms in the call:
>
> calc.calculate()
>
> Then it will work on the atoms object associated with the set_calculator()
> method. Unfortunately, then I get the error:
>
>     calc.calculate()
>   File " /ase/calculators/calculator.py", line 644, in calculate
>     self.write_input(self.atoms, properties, system_changes)
>   File " /ase/calculators/nwchem.py", line 75, in write_input
>     p.initial_magmoms = atoms.get_initial_magnetic_moments().tolist()
> AttributeError: 'NoneType' object has no attribute
> 'get_initial_magnetic_moments'
>
> The reason is that write_input() is called with self.atoms that is None.
> Obviously the calculator does not have atoms object although
> atoms.set_calculator(calc) was called. This is because NWChem class has no
> set_atoms() method. Should we write this one?
>
> I tend to first fix the issue number (2). What about the first issue?
>

The main problem is that calculators are not meant to act as optimizers.

We discussed this for the GULP optimizer, see ase.calculators.gulp,
which solves the problem by returning an object that resembles an ASE
optimizer.  Thus it should also work with other ASE machinery like
NEB, BasinHopping, etc. (Whether they *actually* work in this moment
is a different question, but using an explicit optimizer-like object
means that any problem to be solved.)

Upon reviewing the code in the GULP calculator, I think it would be
more elegant to decorate the get_optimizer method with @classmethod.
Since this is not implemented by very many calculators anyway, we can
streamline it as necessary later.

If it is a classmethod, we can do:

atoms = ...
# The 'opti' keyword makes it run a relaxation:
opt = GULP.get_optimizer(atoms, keywords='opti conp', ....)
# Now the objects are all created and linked: opt ->atoms -> calc
opt.run(fmax=0.05)
calc = atoms.get_calculator()
E = calc.get_potential_energy()

Presently we do

atoms = ...
# The 'opti' keyword makes it run a relaxation:
calc = GULP(keywords='opti conp', ....)
opt = calc.get_optimizer(atoms)
# Now the objects are all created and linked: opt ->atoms -> calc
opt.run(fmax=0.05)
calc = atoms.get_calculator()
E = calc.get_potential_energy()

The gulp_opt.py test tests this, but obviously requires GULP.

Best regards
Ask


> I will appreciate your feedback very much.
>
> Best regards,
> Ivan
>
>
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