[ase-users] ASE LAMMPS: update Atoms object coordinates and use constraints

[Spencer Hills]

Hello,

Here are the relevant portions of the code:

from ase import Atoms, Atom

from ase.io import read,write

from ase.calculators.lammpsrun import LAMMPS


parameters = {'pair_style':'tersoff','pair_coeff':["* *  Au.tersoff
Au"],'boundaries':'p p p','mass':masses,'minimize':'1.0e-3 1.0e-2 200
4000','run':'0'} #define lammps input file parameters
files=["~/Downloads/Au.tersoff"] #call potential file
calc = LAMMPS(files=files,parameters=parameters) #input to calculator
atoms.set_calculator(calc)  #set calculator
atoms.get_potential_energy() # get energy -> lammps minimize function is
called in in_lammps made by calculator, and minimizes structure based on
lammps force fields (tmp traj files show this)

I am using the multistep minimization that lammpsrun.py uses
(params['minimize']
= 'etol ftol maxiter maxeval', in your example), and was hoping that it
there was a way to get the new coordinates from the lammps trajectory. I am
able to save the trajectory files produced by lammps with ASE (temporary
trajectory files), but have not been able to extract the coordinates from those
files.

I think that with this command that you mentioned, I should be able to get
those new positions (calc.trajectory_out =
Trajectory('/tmp/sio2.run.traj','w')).
Do you have example code of how that works?

Thanks,
Spencer

On Tue, Mar 14, 2017 at 12:34 AM, - <mazay0 at gmail.com> wrote:

> Please, show your code.
> Minimization should be done with  LBFGS,MDMin,FIRE classes from
> ase.optimize. Where do you call minimize() function ?
>
>
> Concerning constraints in LAMMPS input file.
> Right now I work on  this functionality here:
> https://gitlab.com/Mazay0/ase/tree/lammps-multistep
> Currently you can fix atoms with the following parameters of the
> calculator:
>
> params['group'] = ['lower_atoms id ' + ' '.join([str(atom.index+1) for
> atom in sio2 if atom.position[2] < 6 ])] # named group of all atoms if z
> coordinate less than 6.0
> params['fix'] = ['freeze_lower_atoms lower_atoms setforce 0.0 0.0 0.0']  #
> fix their position, in fact you can used any fix from here:
> http://lammps.sandia.gov/doc/fix.html
>
> For a while my code do not consider ASE constraints, but in future I am
> going  to implement automatic generation of fix commands from Atoms's
> constraints.
>
> Also you can control trajectory generation with two parameters of the
> calculator:
>
> calc.trajectory_out = Trajectory('/tmp/sio2.run.traj','w') # convert
> LAMMPS trajectory  from 'trj_xxx' to ASE trajectory '/tmp/sio2.run.traj'
> calc.dump_period = 20   # write trajectory frame each 20 steps
>
> To run multistep simulation just pass the desired number of steps:
>
> params['run'] = 100000
> calc.parameters = params
>
> and call run() method of the calculator:
>
> calc.run()
>
>
> For multistep minimization there is a code in lammpsrun.py that should
> accept something like this:
>
> params['minimize'] = 'etol ftol maxiter maxeval' # see
> http://lammps.sandia.gov/doc/minimize.html for details
>
> But I have not tested it yet.
>
>
>
>
> On 14 March 2017 at 00:28, Spencer Hills via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
>> Hello,
>>
>> I am new to ASE and am trying to use it to look at different data types
>> by calling other functions (ex: LAMMPS). With the ASE atoms object it is
>> very easy to keep everything stored in one place. I am using lammpsrun.py
>> from the standard ASE package to write input files from a code, so that I
>> can make a modular code and not require the user to write lammps input file
>> everytime they want to run the code.
>>
>> However, when I use LAMMPS and call the minimize function, I run into
>> some difficulties. It will minimize the energy correctly (compared to
>> running lammps with the python library version of it and the same inputs),
>> but it does not update the positions of the atoms in the atoms object, so I
>> can't compare the minimized energy to anything else because its a different
>> arrangement.
>>
>> Is there a way to update the atoms object with the LAMMPS minimized
>> structure? I think that I could make it read the trajectory file and
>> convert that to positions, but I would rather not save the temporary files
>> in order to do this. Is there a more elegant way to do this? Or is there a
>> current implementation in ASE?
>>
>> Additionally, when I call the minimize function, it does not use the
>> constraints that I assign to it. Right now I am starting simple with one
>> atom at a fixed position, but this atom does not stay in the same position.
>>
>> Is there a way to pass the constraints to the LAMMPS input file?
>>
>> I've looking through some of the mailing list, and have been unable to
>> find answers to the questions. Any direction, either to previous threads or
>> general help on this issue would be appreciated!
>>
>> Thanks,
>> Spencer Hills
>> Research Aide
>> Argonne National Lab
>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
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>>
>
>
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