added manifest tutorial 8 and fixed 4 and 5

Author: simongravelle

files/tutorial4/.manifest

@@ -20,15 +20,12 @@ solution/create.data
 solution/create.lmp
 solution/create.log
 solution/minimize.data
-solution/minimize.ipynb
 solution/minimize.lmp
 solution/minimize.log
 solution/equilibrate.data
-solution/equilibrate.ipynb
 solution/equilibrate.lmp
 solution/equilibrate.log
 solution/shearing-ions.dat
-solution/shearing.ipynb
 solution/shearing.lmp
 solution/shearing.log
 solution/shearing.png

files/tutorial5/.manifest

@@ -20,7 +20,6 @@ decorate.png
 decorate-Si.histo
 decorate.species
 deform.data
-deform.ipynb
 deform.lmp
 deform.log
 deform-mod.data
@@ -30,7 +29,6 @@ deform-Si.histo
 deform.species
 reaxCHOFe.inc
 relax.data
-relax.ipynb
 relax.lmp
 relax.log
 relax-O.histo

files/tutorial8/.manifest

@@ -0,0 +1,45 @@
+# LAMMPS Tutorial manifest file. This file determines what is downloaded when.
+# comments start with a # as the first character.
+# comments and empty lines are ignored
+##############################################################################
+# 1) input file templates
+# the first file will be automatically loaded
+CNT.data
+mixing.lmp
+M-M_post.mol
+M-M_pre.mol
+M-M.rxnmap
+M-P_post.mol
+M-P_pre.mol
+M-P.rxnmap
+polymerize.lmp
+P-P_post.mol
+P-P_pre.mol
+P-P.rxnmap
+solution
+styrene.mol
+
+# 2) solution files
+# only downloaded on request
+CNT.data
+mixing.log
+mixing.restart
+M-M_pre.mol
+M-P_post.mol
+M-P.rxnmap
+polymerize.log
+P-P_post.mol
+P-P.rxnmap
+mixing.data
+mixing.lmp
+mixing.png
+M-M_post.mol
+M-M.rxnmap
+M-P_pre.mol
+polymerize.data
+polymerize.lmp
+polymerize.png
+P-P_pre.mol
+styrene.mol
+
+# 3) folders not known to LAMMPS GUI will be skipped

lammps-tutorials.tex

@@ -1216,13 +1216,11 @@ \subsubsection{Improving the script}
 \subsection{Tutorial 2: Pulling on a carbon nanotube}
 \label{carbon-nanotube-label}
 
-% "classical" or rather "conventional molecular"?
-% SG: "conventional" is indeed better
 In this tutorial, the system of interest is a small, single-walled
 carbon nanotube (CNT) in an empty box (Fig.~\ref{fig:CNT}).  The CNT is
 strained by fixing atoms at one end and moving atoms at the
 other end with constant velocity.  To illustrate the difference between
-conventional~\cite{typelabel_paper} and reactive force fields, this
+conventional and reactive force fields, this % SG: I am not sure why typelabel_paper was cited here. Am I wrong to remove it?
 tutorial is divided into two parts: in the first part, a conventional molecular force
 field (called OPLS-AA~\cite{jorgensenDevelopmentTestingOPLS1996}) is
 used and the bonds between the atoms of the CNT are unbreakable.  In the