Trajectory momenta

[Nicolas Künzel]

Hello,

I've got a problem when printing out the trajectory. When I want to print out momenta I found in the code that this is just possible in atomic units right now which wouldn't be a problem. But when I just leave the unit brackets {} empty or just don't write them at all I get the following error:

Traceback (most recent call last):

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 101, in <module>

    main(args[0], options.do_yappi)

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 51, in main

    simulation.run()

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/simulation.py", line 219, in run

    o.write()  # threaded output seems to cause random hang-ups. should make things properly thread-safe

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/outputs.py", line 318, in write

    self.system.trajs.print_traj(self.what, self.out, b=0, format=self.format, cell_units=self.cell_units, flush=doflush)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/properties.py", line 2297, in print_traj

    fatom.q = cq

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 802, in __setattr__

    return obj.__set__(self, value)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 614, in __set__

    self.__setitem__(slice(None, None), value=value)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 590, in __setitem__

    self.view(np.ndarray)[index] = value

ValueError: could not broadcast input array from shape (16,3) into shape (3)

The lines I tried in the input file are:

<trajectory filename='momenta.out' stride='1' format='xyz' cell_units='angstrom'> momenta{} </trajectory>

<trajectory filename='momenta.out' stride='1' format='xyz' cell_units='angstrom'> momenta </trajectory>

Or when I try to write atomic units in the brackets it tells me:

Traceback (most recent call last):

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 101, in <module>

    main(args[0], options.do_yappi)

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 51, in main

    simulation.run()

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/simulation.py", line 219, in run

    o.write()  # threaded output seems to cause random hang-ups. should make things properly thread-safe

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/outputs.py", line 318, in write

    self.system.trajs.print_traj(self.what, self.out, b=0, format=self.format, cell_units=self.cell_units, flush=doflush)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/properties.py", line 2281, in print_traj

    cq = self[what]

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/properties.py", line 2264, in __getitem__

    return  unit_to_user(pkey["dimension"], unit, 1.0) * pkey["func"](*arglist,**kwarglist)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/units.py", line 347, in unit_to_user

    return number / unit_to_internal(family, unit, 1.0)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/units.py", line 330, in unit_to_internal

    raise TypeError(base + " is an undefined unit for kind " + family + ".")

TypeError: atomic units is an undefined unit for kind momentum.

Doing the same with positions and the right units (angstrom) in the brackets that works well.

Am I doing something wrong?

Kind regards

Nicolas Künzel

[venkat kapil]

Hello Nicolas, 

I tried these and I get the same output without any error.

<trajectory filename="pos" stride="1" format='xyz' cell_units='angstrom'> momenta{} </trajectory>

<trajectory filename="pos" stride="1" format='xyz' cell_units='angstrom'> momenta </trajectory>

<trajectory filename="pos" stride="1" format='xyz' cell_units='angstrom'> momenta{atomic_unit} </trajectory>

Note that I specified "atomic_unit" and not  "atomic_units". 

Can you share with me your input.xml that gave you the error:

Traceback (most recent call last):

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 101, in <module>

    main(args[0], options.do_yappi)

  File "/data/nk158/i-PI-dev/trunk/bin/i-pi", line 51, in main

    simulation.run()

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/simulation.py", line 219, in run

    o.write()  # threaded output seems to cause random hang-ups. should make things properly thread-safe

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/outputs.py", line 318, in write

    self.system.trajs.print_traj(self.what, self.out, b=0, format=self.format, cell_units=self.cell_units, flush=doflush)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/engine/properties.py", line 2297, in print_traj

    fatom.q = cq

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 802, in __setattr__

    return obj.__set__(self, value)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 614, in __set__

    self.__setitem__(slice(None, None), value=value)

  File "/cluster/data/nk158/i-PI-dev/trunk/ipi/utils/depend.py", line 590, in __setitem__

    self.view(np.ndarray)[index] = value

ValueError: could not broadcast input array from shape (16,3) into shape (3)

Also, are which version / branch of i-pi are you using  ?

Best,
Venkat

[Michele Ceriotti]

Dear Nicolas, 

    I should add: units are a sore point in i-PI, and there is a branch in which we're trying to fix things once and for all. If you want to contribute to the code, and/or to share your thoughts, that is a very good place to start. https://github.com/cosmo-epfl/i-pi-dev/pull/188

Thanks

[Nicolas Künzel]

Oh sorry, forgot to write that. I am using the code from i-PI-dev/trunk right now.

The input file which gave the error is actually RESTART file which I modified for which new trajectory output:

<simulation>

   <total_steps>999999</total_steps>

   <output prefix=''>

      <trajectory filename='momenta_equi.out' stride='100' format='xyz' cell_units='angstrom'> momenta </trajectory>

      <trajectory filename='positions_equi.out' stride='100' cell_units='angstrom'>positions{angstrom}</trajectory>

      <checkpoint stride='100' overwrite='False' filename='harm.checkpoint'>1</checkpoint>

      <properties filename='harm.out' stride='1000' shape='(6)'>

       [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin},

         potential{kelvin} ]

      </properties>

   </output>

   <prng>

      <set_pos>224</set_pos>

      <state shape='(624)'>

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      </state>

      <seed>12345</seed>

   </prng>

   <ffsocket mode='unix' name='driver'>

      <address>harmonic</address>

   </ffsocket>

   <system>

   <cell shape='(3, 3)'>

       [   7.12300000e+01,   4.36157958e-15,   4.36157958e-15,   0.00000000e+00,   7.12300000e+01,

           4.36157958e-15,   0.00000000e+00,   0.00000000e+00,   7.12300000e+01 ]

      </cell>

      <beads natoms='1' nbeads='16'>

         <q shape='(16, 3)'>

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         </q>

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              5.90233480e+00,   1.83208315e+00,  -6.92933954e-01,   5.23644409e+00,   5.97102040e+00,

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              1.30851589e+01,  -3.39038136e+00,  -4.78007603e-01 ]

         </p>

         <m shape='(1)'> [   1.83736223e+03 ] </m>

         <names shape='(1)'> [ H ] </names>

      </beads>

      <motion mode='dynamics'>

         <dynamics mode='nvt'>

            <timestep>  1.24024119e-01</timestep>

            <nmts shape='(1)'> [ 1 ] </nmts>

            <thermostat mode='langevin'>

               <tau>  1.03353433e+03</tau>

               <ethermo> -4.47895941e-01</ethermo>

            </thermostat>

         </dynamics>

      </motion>

      <forces>

         <force forcefield='driver'>

         </force>

      </forces>

      <ensemble>

         <temperature>  9.50044560e-04</temperature>

      </ensemble>

   </system>

</simulation>

[Nicolas Künzel]

I tried to use the inputs you are writing there and I get the same error again.

[Michele Ceriotti]

This is weird. Since there is no "trunk" branch I assume you are using i-pi-dev/master. Are you sure there isn't something silly like input encoding messing up some of the special characters, etc?

I tried Venkat's example, and works flawlessly here.

[Nicolas Künzel]

Ok,
I think I just download i-PI again and set it up new. Which branches would you recommend? I guess the master branch would be the right one?

Before I checked out the i-pi-dev via svn from github and in the resulting folder there are two folders: branches and trunk.
I thought the trunk folder would be the right one to work in since in the branches folder there is no master folder.

But I just download the master branch now as zip file and then that should work.

[Nicolas Künzel]

I am now using the i-pi-master branch and getting the same error.

But I realized that it first happens, when I connect the driver code. Just the reading of the input file works but when connecting the driver in order to start the MD run I get this error.
I tried it in the examples/harmonic/ right now.

[Nicolas Künzel]

Could that be a problem with the python version or the installation on our server?

[venkat kapil]

I tried your input and got the same error. 

[Michele Ceriotti]

OK, so there is a minimal working example. Looks like a very weird bug, all the other inputs are working just fine. At this point it's probably best you file a bug on github so we can track it from there.

[Nicolas Künzel]

Ok. I have done that.
So until then I won't be able to check the momentum distributions for my calculations?

[Nicolas Künzel]

Thanks to Venkat Kapil the issue got fixed.

Thanks!

[Michele Ceriotti]

Ah! I see what was the problem. We got a bit sidetracked by the unrelated atomic_unit/atomic_units initial bug. OK, glad this got solved without even having to file a bug. 

[venkat kapil]

@Ceriotti: actually this went through the full process of filing a bug, opening a pull request, fixing it and closing the issue, just that it was a quick fix.

Thanks Nicolas for finding the bug.