Request for more info

[EnthusiasticTeslim]

Thank you for the great code. I am trying to use it to diffusivity of O (in water molecules). Following your approach, I dump the trajectory as follows:

dump 2 all custom 2000 dump_npt_step04.lammpstrj id mol type x y z vx vy vz

See the data file here (https://file.io/u989fgFsemUj). I used moltemplate to create the lammp input files. How do I go about specifying the --mol and --nummol for my system. Thanks.

For a water system with 6420 water molecules, I tried :

python PyLAT.py -T 300 --nummol 2140 --mol OW --nummol 4280 --mol HW -d -v 2 log.lammps npt_stp04.data dump_npt_step04.lammpstrj

and got the following error:

beginning COM calculation
COM calculation 100.00% complete
beginning MSD calculation
unwrap complete
Traceback (most recent call last):
  File "/home/romagnolilab/Documents/ml-md-project/data/water/04_NPT/mol/../../../PyLAT/PyLAT.py", line 306, in <module>
    output = m.runMSD(comx, comy, comz, Lx, Ly, Lz, Lx2, Ly2, Lz2, moltype, moltypel, dt, tsjump, output, ver, arg.MSD_skip, arg.MSD_num_init)
  File "/home/romagnolilab/Documents/ml-md-project/data/PyLAT/src/MSD.py", line 51, in runMSD
    MSD = self.MSDadd(r2, MSD, molcheck, i, j)
  File "/home/romagnolilab/Documents/ml-md-project/data/PyLAT/src/MSD.py", line 122, in MSDadd
    sr2 = np.dot(r2, molcheck[k])
  File "<__array_function__ internals>", line 5, in dot
ValueError: shapes (2140,) and (6420,) not aligned: 2140 (dim 0) != 6420 (dim 0)

Please advice.