Author Topic: Virtual Nanolab not reading energies and velocity from LAMMPS  (Read 3710 times)

0 Members and 1 Guest are viewing this topic.

Offline leofedep

  • New QuantumATK user
  • *
  • Posts: 1
  • Country: ar
  • Reputation: 0
    • View Profile
Dear all, I followed the steps to import an output from LAMMPS to Virtual Nanolab according to the tutorial (http://quantumwise.com/publications/tutorials/item/825-importing-lammps-trajectories-into-vnl). However, although the output (log.lammps) has the energies in the way recommended (step temp pe etotal press), the "Movie Tool" does not read them, instead appears "No data available".  But, it does show the timesteps structures. On the other hand, the "MD Analyzer" has the options like kinetic energy distribution or velocity distribution greyed out. Here the LAMMPS input:
Code
#------1.Initialization--------
clear
[color=red]units            metal[/color]
dimension        3
boundary         p p p 

#------2.Atom definition-------
read_data        pt-pd.data

#------3.Settings--------------
pair_style      eam
pair_coeff       * * ptu6.eam
pair_coeff       * * pdu6.eam

neighbor        0.3 bin # 0.3 Ang for units=metal
neigh_modify    delay 0 every 1 check yes

velocity        all create 300.0 123456 dist gaussian

#------4.Run a simulation------
#------4.1.Minimization--------
fix             1 all nve
[color=red]dump            1 all custom 1 trajectory.dat id type x y z vx vy vz[/color]

thermo          1 
[color=red]thermo_style    custom step temp pe etotal press[/color]

run             1000 
Thanks in advance :)

Offline Julian Schneider

  • QuantumATK Staff
  • QuantumATK Guru
  • *****
  • Posts: 164
  • Country: dk
  • Reputation: 25
    • View Profile
Re: Virtual Nanolab not reading energies and velocity from LAMMPS
« Reply #1 on: January 4, 2016, 14:20 »
From the missing energy data in the MovieTool, I suppose the corresponding LabFloor item is a Trajectory instead of an MDTrajectory object, correct?

From the input file you posted everything looks ok, and the LAMMPS trajectory should be loaded as an MDTrajectory.
It is difficult to find the error without more information or the remaining files.
Is the original "pt-pd.data" file present in the current directory?
Are the atoms in the MovieTool displayed as the correct elements?
Did you rename any of the output files?