Merge pull request #118 from MobleyLab/doi

Remove duplicated references

Author: davidlmobley

README.md

@@ -19,6 +19,7 @@ The current focus is on MD; Monte Carlo (MC) will be addressed in a separate doc
 - Avisek Das (helped with outline and early brainstorming/planning of this document)
 - Victoria Tran Lim provided [valuable editorial feedback](https://github.com/MobleyLab/basic_simulation_training/issues/89#issue-351693860) on the document
 - Michael Shirts caught a variety of typos and other minor issues, and suggested some improvements.
+- Emmanuel Karagiorgos caught some duplicated references
 
 ## Paper writing as code development
 <!-- This discussion is so that people know how to contribute to your document. -->
@@ -39,3 +40,4 @@ This work has not yet been formally published at LiveCoMS; however, you can cite
 - Nov. 5-6, 2018: Make editorial revisions suggested by peer reviewers and Victoria Lim.
 - Nov. 23, 2018: Check references using [`fixbibtex`](https://github.com/jaimergp/fixbibtex), incorporate fixes for problems it caught; addresses a number of typos/missing references caught by Michael Shirts.
 - Nov. 28, 2018: Add DOI, include citation to Grossfield et al. LiveCoMS article with DOI.
+- Dec. 18, 2018: Fix dupliated references.

paper/basic_training.bib

@@ -88,21 +88,6 @@ @book{DillBook
  edition = "Second"
 }
 
-@book{McQuarrieStatMechBook,
- author = "McQuarrie, Donald A.",
- title = "Statistical Mechanics",
- year = "2000",
- publisher = "University Science Books",
-}
-
-@book{ChandlerBook,
- author = "Chandler, David",
- title = "Introduction to Modern Statistical Mechanics",
- year = "1987",
- publisher = "Oxford University Press",
- edition = "First"
-}
-
 @article{thermostatAlgorithms2005,
   title={Thermostat algorithms for molecular dynamics simulations},
   author={H{\"u}nenberger, Philippe H},
@@ -115,12 +100,6 @@ @article{thermostatAlgorithms2005
   publisher={Springer}
 }
 
-@book{allenTildesleyLiquids,
-  title={Computer simulation of liquids},
-  author={Allen, Michael P and Tildesley, Dominic J},
-  year={2017},
-  publisher={Oxford university press}
-}
 
 
 @article{hoover1985canonical,

paper/basic_training.pdf

@@ -862,7 +862,7 @@ \subsubsection{Background and How They Work}
 
 Much of the background information on barostats is analogous to thermostats.
 The pressure of a molecular dynamics simulation is commonly measured using the virial theorem (an expectation value relating to positions and forces)~\cite{ShellNotes, LeachBook}.
-When pairwise interactions and periodic boundary conditions are considered, different approaches are often utilized~\cite{allenTildesleyLiquids, tuckermanBook, ShellNotes}.
+When pairwise interactions and periodic boundary conditions are considered, different approaches are often utilized~\cite{allen_computer_2017, tuckermanBook, ShellNotes}.
 Regardless, these formulas give pressure as a time-averaged quantity, similar to the temperature.
 If we use these formulas to calculate the pressure for a single snapshot, this quantity is referred to as the instantaneous pressure.
 The instantaneous pressure will not always be equal to the target pressure; in fact, in the NPH and NPT ensembles, the instantaneous pressure should undergo fluctuations around the target pressure.
@@ -1004,7 +1004,7 @@ \subsubsection{Deterministic integrators}
 \subsubsection{Stochastic integrators}
 
 Stochastic dynamics simulations include application of a random force to each particle, and represent discretizations of either Langevin or Brownian dynamics.
-A detailed description of such stochastic dynamics may be found in McQuarrie~\cite{McQuarrieStatMechBook}, Chapter 20.
+A detailed description of such stochastic dynamics may be found in McQuarrie~\cite{McQuarrie:2000:}, Chapter 20.
 As detailed in Section \ref{sec:thermostats}, it is common to apply temperature control through the use of Langevin dynamics.
 As a brief aside, this highlights the fact that the choice of integrator is often tightly coupled to the choice of thermostat and/or barostat.
 Different combinations may demonstrate better performance and for expanded ensemble methods it is necessary to utilize an integrator specific to the selected temperature- or pressure-control algorithm.