Frequently Asked Questions
**************************


There are no reactions
======================

* Increase the temperature

* **NanoReactor**: Increase "DiffusionTime", set "MinVolumeFraction"
  to a smaller value, set "InitialRadius" to a smaller value

* **LatticeDeformation**: Set "MinVolumeFraction" to a smaller value,
  decrease "Period"

* Set "MolecularDynamics UseDeuterium=No"

* Ensure that you use a reactive potential (e.g. ReaxFF, DFTB,
  MLPotential)

Note: The best value for "MinVolumeFraction" depends on the initial
density ("MolecularDynamis%BuildSystem%Density").  If you decrease the
initial density, you may need to also decrease the
"MinVolumeFraction".

Tip:

  Run the simulation with the fast UFF force field to get a feeling
  for if the initial settings are reasonable. With UFF no reactions
  will happen but you can still see how the density fluctuates in the
  MD simulation.


There are too many reactions
============================

* Decrease the temperature

* **NanoReactor**: Decrease "DiffusionTime", set "MinVolumeFraction"
  to a larger value, set "InitialRadius" to a larger value

* **LatticeDeformation**: Set "MinVolumeFraction" to a larger value,
  increase "Period"

* Set "MolecularDynamics UseDeuterium=Yes"

Note: The best value for "MinVolumeFraction" depends on the initial
density ("MolecularDynamis%BuildSystem%Density").  If you decrease the
initial density, you may need to also decrease the
"MinVolumeFraction".


The MD simulations are too slow
===============================

* Decrease the number of atoms

* Decrease the number of NanoReactor or LatticeDeformation cycles

* Increase the MD time step


How should I set the density and compression factor?
====================================================

* **Nanoreactor**: The density should be approximately the normal
  liquid density of your system, with a compression factor of about
  0.5-0.7

* **Lattice deformation**: The density should be about half the normal
  liquid density of your system, with a compression factor of about
  0.15-0.30


The simulation explodes
=======================

* Follow the steps for *There are too many reactions*.

* Decrease the MD time step


How do I use computing resources efficiently?
=============================================

The steps are parallelized as follows:

* MolecularDynamics runs as many jobs in parallel as possible,
  respecting the allocation ("NSCM")

* NetworkExtraction runs "NumSimulations" ChemTraYzer2 jobs
  sequentially in serial; then "NSCM" geometry optimizations and
  single points are run in parallel.

* ProductRanking runs in serial

Thus, most of the computational steps except ProductRanking are run
efficiently in parallel. You may thus choose to set "ProductRanking
Enabled=False" if you have a large node allocated, and then restart
from the previous results using "ProductRanking Enabled=True" on a
smaller allocation.
