Problem running lammps using python script: Random failures

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1

Hi All,

I am trying to run an initial lammps script in python, and then use a loop
to extract the velocities after running for 32 timesteps. However, after
the initial lammps script is run *sometimes* the loop used for extraction
fails, that is, the simulation does not actually run, and is seen by
unchanging thermodynamic data. Whether it works or not seems to be
stochastic.

Here is the python script used to first run the lammps script and loop:
https://github.com/ntpl/ntpy/blob/master/examples/nmdpar/nmd.proc.simple

Here is the initial lammps script that is run first:
https://github.com/ntpl/ntpy/blob/master/examples/nmdpar/lammps.template

Here is the output for when it works:
https://github.com/ntpl/ntpy/blob/master/examples/nmdpar/py_working.txt
    - Line 94, it can be seen that the simulation advances.

Here is the output for when it fails:
https://github.com/ntpl/ntpy/blob/master/examples/nmdpar/py_fail.txt
    - Line 94, it can be seen that the simulation does not advance.

Thank you for your time,
Kevin Parrish

2

Hi All,

I am trying to run an initial lammps script in python, and then use a loop
to extract the velocities after running for 32 timesteps. However, after
the initial lammps script is run *sometimes* the loop used for extraction
fails, that is, the simulation does not actually run, and is seen by
unchanging thermodynamic data. Whether it works or not seems to be
stochastic.

you have warnings that i find quite troublesome in your output, even
when it works. have you investigated what those mean?

there may be an incompatibility. how did you compile the python wrapper?
what OS/CPU are you on? do you run a 32-bit or a 64-bit version of LAMMPS?

axel