Add references relating to timestep, issue 109

Author: davidlmobley

paper/basic_training.bib

@@ -1116,3 +1116,42 @@ @article{Palmer2018
 year = {2018},
 doi = {10.1063/1.5029463},
 }
+
+
+@article{Martinez:2009:JournalofComputationalChemistry,
+  title = {{{PACKMOL}}: A Package for Building Initial Configurations for Molecular Dynamics Simulations.},
+  volume = {30},
+  doi = {10.1002/jcc.21224},
+  language = {English},
+  number = {13},
+  journal = {J. Comp. Chem.},
+  author = {Mart\'inez, L and Andrade, R and Birgin, E G and Mart\'inez, J M},
+  month = oct,
+  year = {2009},
+  keywords = {logP Paper,SAMPL5},
+  pages = {2157--2164},
+  pmid = {19229944}
+}
+
+@misc{Jewett:2018:moltemplate,
+  title = {Moltemplate},
+  howpublished = {https://www.moltemplate.org/},
+  journal = {moltemplate},
+  author = {Jewett, Andrew},
+  month = nov,
+  year = {2018},
+}
+
+@article{Hirel:2015:ComputerPhysicsCommunications,
+  title = {Atomsk: {{A}} Tool for Manipulating and Converting Atomic Data Files},
+  volume = {197},
+  issn = {0010-4655},
+  shorttitle = {Atomsk},
+  doi = {10.1016/j.cpc.2015.07.012},
+  journal = {Computer Physics Communications},
+  author = {Hirel, Pierre},
+  month = dec,
+  year = {2015},
+  keywords = {Atomistic simulations,Dislocation,File conversion,Nye tensor,Polycrystal},
+  pages = {212-219},
+ }

paper/basic_training.pdf

@@ -1017,7 +1017,7 @@ \subsubsection{Choosing an appropriate timestep}
 For all-atom simulations with constraints on the high-frequency bonds, timesteps can be commonly increased to 2 fs; coarse-grained simulations with particles of higher mass and smaller force constants can have much larger timesteps.
 After choosing a timestep, a test simulation should be run in the microcanonical ensemble to ensure that the choice of timestep yields dynamics that conserve energy.
 The timestep should also be short enough that properties calculated from the simulation, regardless of ensemble, are independent of the chosen timestep.
-This is because an inappropriately large timetep can lead to subtle changes to the ensemble being simulated and alter computed thermodynamic and transport properties, especially in stochastic simulations or those coupled to thermostats or barostats.
+This is because an inappropriately large timetep can lead to subtle changes to the ensemble being simulated~\cite{LeachBook, allen_computer_2017} and alter computed thermodynamic and transport properties, especially in stochastic simulations or those coupled to thermostats or barostats~\cite{Fass2018}.
 Methods also exist to increase the timestep beyond the limit imposed by the system's highest-frequency motion.
 Some examples of these enhanced timestepping algorithms include multiple-timestep methods which separately integrate high-frequency motion from low-frequency motion and schemes which repartition atomic masses to decrease the highest-frequency motion seen in the system\cite{Berne:1999:Molecular,Hopkins:2015:JCTC:Long}.