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General Questions and Answers / Virtual Nanolab not reading energies and velocity from LAMMPS

« on: December 28, 2015, 20:01 »

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