Closed hgandhi2411 closed 3 years ago
@hgandhi2411 this is really great work, nice job Heta! Is there anyway though you can remove the notebook output from the log file? It makes the log files hard to read.
@hgandhi2411 this is really great work, nice job Heta! Is there anyway though you can remove the notebook output from the log file? It makes the log files hard to read.
Thanks @whitead. I can look into clearing out the notebook output.
@whitead In the 08. N-Body Neural Force Fields.ipynb
notebook, the following error shows up occasionally and disappears on re-running the notebook. Do we need to worry about it?
########### Hoomd-Sim Code ################
hoomd.context.initialize('--mode=cpu')
tfcompute = htf.tfcompute(model)
# create a square lattice
system = hoomd.init.create_lattice(unitcell=hoomd.lattice.sq(a=1.2),
n=[16,16])
nlist = hoomd.md.nlist.cell()
# NVT ensemble
hoomd.md.integrate.mode_standard(dt=0.001)
hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=0.1, tau=0.5).randomize_velocities(seed=1)
tfcompute.attach(nlist, r_cut=5, save_output_period=5)
#run with our silly model
hoomd.run(1e3)
------------------
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-1-127d1819638d> in <module>
13 tfcompute.attach(nlist, r_cut=5, save_output_period=5)
14 #run with our silly model
---> 15 hoomd.run(1e3)
/usr/share/miniconda/lib/python3.7/site-packages/hoomd/__init__.py in run(tsteps, profile, limit_hours, limit_multiple, callback_period, callback, quiet)
199 if not quiet:
200 context.msg.notice(1, "** starting run **\n");
--> 201 context.current.system.run(int(tsteps), callback_period, callback, limit_hours, int(limit_multiple));
202 if not quiet:
203 context.msg.notice(1, "** run complete **\n");
RuntimeError: Error computing cell list
RuntimeError: Error computing cell list
Error: Process completed with exit code 1.
@whitead Now only errors are logged when notebooks are run. Let me know if you'd like any other changes.
@hgandhi2411 that is bizarre, especially since it uses a random number seed. Can you try adjusting the check period nlist.cell(check_period=1)
?
@hgandhi2411 looks like there are some build errors still
@whitead Everything works now!