Number of RDF timesteps requested longer than simulation.

[ferjcarmona]

Hi,

I'm getting this error when specifying what timesteps to use for an rdf calculation with --RDF_Timesteps.

The simulation is 15 ns and I wanna use the last 2 ns. The simulation timestep is 1 fs. This is how I'm calling PyLAT.

python PyLAT.py -g --RDF_Timesteps 2000000 --mol TF2 --mol C2M --nummol 170 --nummol 170 -p /scratch365/fcarmona/LANL_Tg_Study/Emim_NTf2_Tg_study/dynamics/170K/ -f 170_rdf.json -v 2 Emim_NTf2.log Emim_NTf2.data Emim_NTf2.lammpstrj

When executed this is the output I get.

COM calculation 100.00% complete
Number of RDF timesteps requested longer than simulation. Using all timesteps.
beginning RDF calculation
RDF calculation complete
beginning file generation
file generated

I am not sure why it is using all timesteps. The only abnormality I can think off is in my log file where the thermostyle is outputting temperature first and then the timestep.

Please advise,

Thank you!

[mike5603]

In this case the timesteps refer to the timesteps saved in the trajectory file so you should divide your number of timesteps by the frequency you are saving your trajectory file.

[ferjcarmona]

Hi!

Got it, now it's working thanks.

Also is there a way to specifically tell PyLAT to use specific frames? As in, from the 150 frames generated use frames 80 to 100.

[mike5603]

As of now, there is no way to specify the steps used. Probably wouldn't be too terrible to implement yourself. You would just need to add a couple of parameters such as start and finish, and then use those when performing the slicing on lines 71-73 of src/COMradial.py. You would also need to adjust the normalization to get the correct result