Messages

1

General Questions and Answers / Re: VNL for LAMMPS

« on: April 6, 2016, 16:05 »

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!

2

General Questions and Answers / VNL for LAMMPS

« on: April 5, 2016, 19:29 »

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