Closed chrisjonesBSU closed 4 years ago
Reading this: https://groups.google.com/g/hoomd-users/c/nVSCQtcTCzc?pli=1
Some possible places to start looking:
So far, I've been using r_cut = 1.2
Also, the systems are initialized with a large box (calculated volume edge length * 5) to allow for PACKMOL to pack.
Looking at the simulations that did run, I think something is wrong/off with the calculation of box edge lengths as a function of density and system mass _calculate_L()
in simulate.py
. The final systems are very non-dense..
After testing a couple things out on a new branch, I think the memory error was related to having such a large initial box size. Now I'm dealing with particle-out-of-box errors, but I'll close this issue for now.
I haven't done any bench marking to see at what system size the error occurs, but I am getting it with relatively small systems around 20,000 atoms.
I wonder if its related to using the
hoomd_simulation.py
method available withinmbuild
.This is the current process:
Generate an mbuild compound of the system Using foyer to type this compound, we get a parmed structure Initialize a hoomd simulation from the parmed structure.