Messages

1

General Questions and Answers / Re: About visualizing lammps output

« on: May 26, 2016, 19:22 »

Hi Julian,

Thanks for letting me know.

For the velocity distribution calculation, do you use the magnitude of the velocity vector of each atoms at each time step and compute the average over the selected time span ? Also is f(v) on the Y axis the number of atoms and not number of atoms divided by the total number? Is there any way I can alter the velocity distribution plot to show the latter quantity?

Thank you,
Stephen Thomas.

2

General Questions and Answers / About visualizing lammps output

« on: May 25, 2016, 21:16 »

Hi,

I am trying to use the MD Analyzer to visualize the velocity distribution of a LAMMPS output. If I dump "all" the atoms from the lammps simulation using:

dump            d_trajectory all custom 100 trajectory.dat id type x y z vx vy vz

 everything works fine, but if I select a subset of atoms using

dump            d_trajectory subsetgroup custom 100 trajectory.dat id type x y z vx vy vz

, I get the following error while trying to plot the velocity distribution:

Traceback (most recent call last):
  File "./zipdir/NL/GUI/MainWindow/LabFloor/LabFloorModel.py", line 239, in load
  File "/home/sthomas/QuantumWise/VNL-ATK-2015.1/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSLabFloorPlugin.py", line 67, in load
    data = reader.getTrajectory(filename)
  File "/home/sthomas/QuantumWise/VNL-ATK-2015.1/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSReader.py", line 390, in getTrajectory
    velocities_present)
  File "/home/sthomas/QuantumWise/VNL-ATK-2015.1/lib/python2.7/site-packages/AddOns/LAMMPSPlugins/Filters/LAMMPSReader.py", line 601, in _getPositionsAndElements
    raise NLFileError("Incorrect file line found: %s" % (traj_file_content[line_number]))
NLFileError: Incorrect file line found: 577 1 1.35125 -14.8637 6.75625 -0.00295542 0.000169555 0.00180072

Kindly let me know if there is a way to analyze a subset of the atoms?

Thank you,
Stephen Thomas.