I’m using LAMMPS-17Nov16 to simulate shock propagation in an all-atom polyurea model, with preliminary minimization and equilibration using an NPT ensemble, and have a few questions:
I apply periodic boundary conditions (BCs) in all directions during equilibration
(‘boundary p p p’),
but subsequently apply non-periodic BCs along the direction of shock propagation
(‘change_box all boundary p p sf remap units box’).
The original all-atom model was generated by someone else using Materials Studio, and I’m confident there are no bonds crossing the cell boundaries at the start (before minimization). Is there something I should check before changing the BCs?
The log file for the simulation contains the message “WARNING: Fix qeq/reax CG convergence failed after 200 iterations at 50047 step
(…/fix_qeq_reax.cpp:722)” for multiple timesteps of shock propagation.
I will try changing the velocity of the wall in the ‘fix wall/piston’ command (it’s 1.5 A/fs), and check the force-field using a different simulation (constant engineering strain), but is there a way to change the number of iterations mentioned?
This question is more general. In the “real” system of units in LAMMPS, the unit of pressure would be (1 kcal/mol-A / 1 A^2) or approx. 69,500 bar. Since the unit of pressure is called atm, do I understand I should divide a reported pressure of, say, 1800 atm by 69,500 to get the actual value?
I’d appreciate any help on these questions; I’m new to LAMMPS.