[ase-users] LAMMPS Trajectory dump file to extendedXYZ custom parameters

[Noam Bernstein]

I don't believe that the LAMMPS dumps reader can parse saved energies. I'm not even sure the column names for those are fixed by LAMMPS.  It would probably be straightforward to extend it to save all the columns to similarly named per-atom properties without knowing what they mean.  It would be possible to hardwire column names to derive per-configuration properties by summing those per atom properties, but it would be nearly as easy to do that summing afterwards in python code or even 
ase convert -e "atoms.info <http://atoms.info/>['lammps_energy'] = sum(atoms.arrays['c_keng']) in.xyz out.xyz <http://out.xyz/>

							Noam

> On Jun 2, 2020, at 3:54 PM, Abhijeet Dhakane via ase-users <ase-users at listserv.fysik.dtu.dk> wrote:
> 
> Hello,
> 
> I have lammps dump file (trajectory) in following format.
> 
> ITEM: TIMESTEP
> 501000
> ITEM: NUMBER OF ATOMS
> 1000
> ITEM: BOX BOUNDS pp pp pp
> 0.0000000000000000e+00 2.7500000000000000e+01
> 0.0000000000000000e+00 2.7500000000000000e+01
> 0.0000000000000000e+00 2.7500000000000000e+01
> ITEM: ATOMS type x y z fx fy fz c_keng c_eng mass id
> 1 0.161303 -0.13692 27.4967 -0.518958 1.44351 -0.998551 0.289493 -4.13849 28.0855 1
> 1 27.431 2.76982 2.67355 1.14793 1.2093 -1.8261 0.222894 -4.15074 28.0855 2
> 1 2.69197 0.0907951 2.74186 -0.521011 -1.17696 0.372958 0.0206195 -4.19658 28.0855 3
> 1 2.96499 2.72915 27.4866 -0.700047 2.33357 -0.243868 0.0588419 -4.15339 28.0855 4
> 1 1.54352 1.52626 1.25266 -2.29776 -1.56517 1.26088 0.00662306 -4.16613 28.0855 5
> 1 1.28417 4.2658 3.94474 -0.135306 -2.28732 -0.254315 0.106935 -4.16458 28.0855 6
> 1 4.28623 1.24612 3.93235 0.0519921 2.10204 0.47689 0.103425 -4.16945 28.0855 7
> 1 4.29929 4.20633 1.40497 1.28975 -2.11527 -1.39339 0.114491 -4.13871 28.0855 8
> 1 5.19262 27.2979 0.0463334 2.04882 1.38252 -1.03927 0.141494 -4.14959 28.0855 9
> 1 5.79476 2.5993 2.56687 -3.07517 1.84936 1.97585 0.388581 -4.10221 28.0855 10
> 
> I would like to convert given dump file into extend XYZ with the sum of "c_keng" parameter (column variables) in the comment (header of extXYZ) like of extendedXYZ like as follow:
> 1000
> Lattice="27.5 0.0 0.0 0.0 27.5 0.0 0.0 0.0 27.5" Properties=species:S:1:pos:R:3:c_keng:R:1:c_eng:R:1:forces:R:3 energy="_JSON 0.0" instead  energy="sum of array (c_keng) at every frame" pbc="F F F"
> H        0.18799400      -0.02854550      27.35690000       0.16047400      -4.25133000       0.19925900       0.15968700       1.18709000
> H        0.42149800       2.65156000       3.08710000       0.05051810      -4.11243000      -2.42461000      -0.67427300      -1.70113000
> H        2.93800000       0.06241060       2.69486000       0.08774280      -4.02904000       0.95560500      -1.66023000       1.78616000
> H        2.71791000       2.48304000      27.64030000       0.27919900      -4.07487000       1.45015000       2.73423000      -1.49880000
> H        1.47313000       1.20343000       1.47406000       0.37260300      -4.13500000      -1.40448000       0.25985600      -0.07530590
> H        1.53047000       4.27182000       4.17967000       0.02550600      -4.18544000      -0.08961830       0.43731600       1.42851000
> H        4.10151000       1.65867000       4.17805000       0.31862200      -4.21833000       0.06896430      -2.31936000      -0.77822000
> H        4.19290000       4.05041000       1.43974000       0.22438900      -4.15162000      -1.57299000       0.40202600       0.14793200
> 
> How should I proceed? I can able to make a sum of the c_keng by using get_array function but how should I implement it for entire trajectory?
> 
> Thanks,
> Abhijeet
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____________
||
|U.S. NAVAL|
|_RESEARCH_|
LABORATORY
Noam Bernstein, Ph.D.
Center for Materials Physics and Technology
U.S. Naval Research Laboratory
T +1 202 404 8628  F +1 202 404 7546
https://www.nrl.navy.mil <https://www.nrl.navy.mil/>
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