[ase-users] [ase-developers] Adjusting atom.momentum?

[Jens Jørgen Mortensen]

On 10/24/2016 12:44 PM, Ask Hjorth Larsen wrote:
>
> Hello
>
> It can access the array and modify it, knowing its own index in the 
> atoms object.
>

Problem is that the Atoms object doesn't have a momenta array.  So, 
"atoms[2].momentum" will create a fresh array with "np.zeros(3)" :-(

     https://gitlab.com/ase/ase/issues/3

Jens Jørgen

> Or is there something more to it?
>
> Actually I guess it is still tricky to handle the case where someone 
> sets the momenta after creating the Atom
>
> Best regards
> Ask
>
>
> El 24 oct. 2016 7:43, "Jens Jørgen Mortensen" <jensj at fysik.dtu.dk 
> <mailto:jensj at fysik.dtu.dk>> escribió:
>
>     On 10/23/2016 01:27 AM, Ask Hjorth Larsen wrote:
>
>         Hello
>
>         An Atom now has a reference to the Atoms from which it was
>         extracted.
>
>         Therefore this is trivial to fix now.  It only requires the
>         will to do so.
>
>
>     What has happened that makes it trivial to fix now and how would
>     you do it?
>
>     Jens Jørgen
>
>
>         Best regards
>         Ask
>
>         2015-10-19 9:37 GMT+02:00 Jens Jørgen Mortensen
>         <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>:
>
>             On 10/16/2015 09:46 PM, Peterson, Andrew wrote:
>
>             In writing the NVE test for the Hookean constraint, I
>             noticed that modifying
>             the momentum attribute of an atom was not permanent. E.g.,
>
>             In [1]: from ase.structure import molecule
>             In [2]: atoms = molecule('CH4')
>             In [3]: atoms[2].momentum[1] += 8.
>             In [4]: atoms.get_momenta()
>             Out[4]:
>             array([[ 0.,  0.,  0.],
>                     [ 0.,  0.,  0.],
>                     [ 0.,  0.,  0.],
>                     [ 0.,  0.,  0.],
>                     [ 0.,  0.,  0.]])
>
>             I know I can use the set_momentum function, but had
>             expected this to behave
>             the same as adjusting a position --- the analogous script
>             with positions
>             does result in changing the position array:
>
>             In [1]: from ase.structure import molecule
>             In [2]: atoms = molecule('CH4')
>             In [3]: atoms[2].position[1] += 8.
>             In [4]: atoms.get_positions()
>             Out[4]:
>             array([[ 0.      ,  0.      ,  0.      ],
>                     [ 0.629118,  0.629118,  0.629118],
>                     [-0.629118,  7.370882,  0.629118],
>                     [ 0.629118, -0.629118, -0.629118],
>                     [-0.629118,  0.629118, -0.629118]])
>
>             Is this how it is supposed to work, or should I file an issue?
>
>
>             I guess you should file an issue.  I really don't know how
>             to fix this.
>             Problem is that the momenta are zero even if you did not
>             explicitly set them
>             and we don't want to allocate an ndarray for them before
>             they become
>             non-zero.  The positions are always backed by an ndarray
>             in the Atoms object
>             ...
>
>             The best I can come of with is to make the ndarray you get
>             from
>             atoms[2].momentum not writeable and document this weird
>             behaviour.
>
>             If the Atoms object already has momenta then it will work
>             fine:
>
>                  atoms[2].momentum = (0, 0, 0)
>                  atoms[2].momentum[1] += 8
>
>             This will actually also work:
>
>                  atoms[2].momentum += (0, 8, 0)
>
>             Jens Jørgen
>
>             thanks,
>             Andy
>
>
>             --
>             Andrew Peterson
>             Assistant Professor
>             Brown University School of Engineering
>             Barus & Holley 247
>             184 Hope Street
>             Providence, RI 02912
>             (401) 863-2153 <tel:%28401%29%20863-2153>
>             http://brown.edu/go/catalyst
>
>
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