VNL for LAMMPS

[lhuang]

Hello,

I am trying to figure out how to use VNL to visualize calculations from Lammps. Here is the error message I received:

Traceback (most recent call last):
  File "./zipdir/NL/GUI/MainWindow/LabFloor/LabFloorModel.py", line 240, in load
  File "/Applications/Virtual NanoLab 2014.3.app/Contents/Resources/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSLabFloorPlugin.py", line 58, in load
    data = reader.getTrajectory(filename)
  File "/Applications/Virtual NanoLab 2014.3.app/Contents/Resources/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSReader.py", line 457, in getTrajectory
    analysis_object._append(ase_atoms_interface, time=float(time.inUnitsOf(Units.fs)), step=frame_index)
  File "./zipdir/NL/Dynamics/MolecularDynamics/MDTrajectory.py", line 108, in _append
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 264, in get_forces
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 142, in _update
  File "/Applications/Virtual NanoLab 2014.3.app/Contents/Resources/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSReader.py", line 477, in _getPotentialEnergy
    raise NLValueError('The LAMMPS log file contains fewer potential energy values than snapshots in the trajectory.')
NLValueError: The LAMMPS log file contains fewer potential energy values than snapshots in the trajectory.

The example I ran is from the EAM example with the distribution.

I was using the lammps version, 10 August 2015.  The VNL is version 2014.3, Mac OS:

System information
Build: 2014.3.ac46a6e
Platform: Darwin
Python 2.7.2
Qt 4.8.5
PyQt 4.10.3
3D graphics - OpenGL
Vendor: Intel
GPU: Intel(R) Iris(TM) Graphics 6100
Version: OpenGL 2.1 INTEL-10.6.33
Shading language version: 1.20
License
Source: Local

Greatly appreciate your time!

Best regards,

Paul

[Jess Wellendorff]

Hi Paul.

We will be happy to help you out here, but it will be much easier if you upload the relevant LAMMPS file(s).

[lhuang]

Sure, I should have done this in the previous message: attached are the files used for the VNL-LAMMPS test. The actual trajectory file is larger than 512 KB. One shall be able to generate it using the "in.eim", "field.eim" and "data.eim" files.

The changes in "in.eim" are suggested by the tutorial:

thermo    10
thermo_style custom step temp press pe etotal

dump atK_traj all custom 10 trajectory.dat id type x y z vx vy vz

Thanks again!

[Julian Schneider]

The problem is that in your log.lammps file, for some reason there are some steps missing between step 260 and 410.
It says

     200    834.82705   -445.10589   -5704.2444   -5488.5326
     210     879.3483   -172.38307   -5712.4813   -5485.2655
     220    922.65357    292.58809   -5720.4329   -5482.0275
     230    937.39042     -62.6088   -5721.3306   -5479.1173
     240    948.08463   -244.98762   -5721.6675    -5476.691
     250    966.14585    442.59564   -5724.4679   -5474.8245
     260    962.51755    581.39448   -5722.3955   -5473.6896      410    827.36123    -897.4114   -5746.4231   -5532.6403
     420    834.65009    31.459134   -5754.7381    -5539.072
     430    821.39706    887.94195   -5758.0841   -5545.8425
     440    777.86776   -258.69939   -5753.6548   -5552.6607

Then, of course the plugin can't find as many energy entries as snapshots in the trajectory, and that's why the error is raised.
I don't know why that happens, but maybe you ran several LAMMPS simulations simultaneously, which wrote to the same logfile.
Try and run the LAMMPS simulation again, and see if the error still persists.
I have attached the log file that I get when I run your simulation and with that logfile everything works fine.