Merge remote-tracking branch 'origin/main' into tutorial-file-revisions

akohlmey · akohlmey · commit 14f39dfa69f3 · 2025-01-05T07:42:40.000-05:00
diff --git a/figures/REACT-reacting.png b/figures/REACT-reacting.png
diff --git a/files/tutorial8/CNT.data b/files/tutorial8/CNT.data
diff --git a/files/tutorial8/M-M_post.mol b/files/tutorial8/M-M_post.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -95,7 +95,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -111,7 +111,7 @@ Charges
      26  0.128800
      27 -0.173400
      28  0.140300
-     29  0.051600
+     29  0.051800
      30 -0.069600
      31  0.035400
      32  0.035400
diff --git a/files/tutorial8/M-M_pre.mol b/files/tutorial8/M-M_pre.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -95,7 +95,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -111,7 +111,7 @@ Charges
      26  0.128800
      27 -0.173400
      28  0.140300
-     29  0.051600
+     29  0.051800
      30 -0.069600
      31  0.035400
      32  0.035400
diff --git a/files/tutorial8/M-P_post.mol b/files/tutorial8/M-P_post.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -123,7 +123,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -139,7 +139,7 @@ Charges
      26  0.128800
      27 -0.173400
      28  0.140300
-     29  0.051600
+     29  0.051800
      30 -0.069600
      31 -0.129000
      32  0.123700
@@ -153,7 +153,7 @@ Charges
      40  0.128800
      41 -0.173400
      42  0.140300
-     43  0.051600
+     43  0.051800
      44 -0.069600
      45  0.035400
      46  0.035400
diff --git a/files/tutorial8/M-P_pre.mol b/files/tutorial8/M-P_pre.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -123,7 +123,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -139,7 +139,7 @@ Charges
      26  0.128800
      27 -0.173400
      28  0.140300
-     29  0.051600
+     29  0.051800
      30 -0.069600
      31 -0.129000
      32  0.123700
@@ -153,7 +153,7 @@ Charges
      40  0.128800
      41 -0.173400
      42  0.140300
-     43  0.051600
+     43  0.051800
      44 -0.069600
      45  0.035400
      46  0.035400
diff --git a/files/tutorial8/P-P_post.mol b/files/tutorial8/P-P_post.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -131,7 +131,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -151,7 +151,7 @@ Charges
      30  0.128800
      31 -0.173400
      32  0.140300
-     33  0.051600
+     33  0.051800
      34 -0.069600
      35 -0.129000
      36  0.123700
@@ -165,7 +165,7 @@ Charges
      44  0.128800
      45 -0.173400
      46  0.140300
-     47  0.051600
+     47  0.051800
      48 -0.069600
      49  0.035400
      50  0.035400
diff --git a/files/tutorial8/P-P_pre.mol b/files/tutorial8/P-P_pre.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -131,7 +131,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
@@ -151,7 +151,7 @@ Charges
      30  0.128800
      31 -0.173400
      32  0.140300
-     33  0.051600
+     33  0.051800
      34 -0.069600
      35 -0.129000
      36  0.123700
@@ -165,7 +165,7 @@ Charges
      44  0.128800
      45 -0.173400
      46  0.140300
-     47  0.051600
+     47  0.051800
      48 -0.069600
      49  0.035400
      50  0.035400
diff --git a/files/tutorial8/solution/polymerize.ipynb b/files/tutorial8/solution/polymerize.ipynb
diff --git a/files/tutorial8/solution/polymerize.lmp b/files/tutorial8/solution/polymerize.lmp
@@ -1,5 +1,5 @@
 # Python script (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -52,7 +52,7 @@ fix rxn all bond/react &
   react R3 all 1 0 5.0 mol5 mol6 P-P.rxnmap
 
 fix mynvt statted_grp_REACT nvt temp 530 530 100
-group CNT molecule 1 2 3
+group CNT molecule 1
 fix myrec CNT recenter NULL 0 0 shift all
 
 thermo 200
diff --git a/files/tutorial8/styrene.mol b/files/tutorial8/styrene.mol
@@ -1,5 +1,5 @@
 # LAMMPS Input File (License CC BY 4.0)
-# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer  
+# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer
 # The DOI will be added upon publication
 # Find more on GitHub: https://github.com/lammpstutorials
 
@@ -63,7 +63,7 @@ Charges
      10  0.128800
      11 -0.173400
      12  0.140300
-     13  0.051600
+     13  0.051800
      14 -0.069600
      15  0.035400
      16  0.035400
diff --git a/lammps-tutorials.tex b/lammps-tutorials.tex
@@ -339,7 +339,7 @@ \subsection{Background knowledge}
   with Applications to Soft Matter} by Jean-Pierre Hansen and Ian Ranald
 McDonald~\cite{hansen2013theory}.  For more resources, the SklogWiki
 platform provies a wide range of information information on statistical mechanics
-and molecular simulations~\cite{sklogwiki_main_page}. 
+and molecular simulations~\cite{sklogwiki_main_page}.
 
 \subsection{Software/system requirements}
 
@@ -498,7 +498,7 @@ \subsubsection{My first input}
 a popular choice for simulations that explore general statistical mechanical
 principles, as it emphasizes relative differences between parameters rather than
 representing any specific material.  The second line, \lmpcmd{dimension 3}, specifies that the simulation is conducted
-in 3D space, as opposed to 2D, where atoms are confined to move only in the 
+in 3D space, as opposed to 2D, where atoms are confined to move only in the
 xy-plane.  The third line, \lmpcmd{atom\_style atomic}, designates
 the atomic style for representing simple, individual particles.
 In this style, each particle is treated as a point with a mass, making it the
@@ -681,7 +681,7 @@ \subsubsection{My first input}
 algorithm~\cite{hestenes1952methods}.  The simulation will stop as soon
 as the minimizer algorithm cannot find a way to lower the potential
 energy. % SG: I don't think that its true, its rather the algorithm
-% will stop when one of the four criteria is met. Axel, what do you think? 
+% will stop when one of the four criteria is met. Axel, what do you think?
 % I propose to replace by "when specific convergence criteria are met"
 Note that, except for trivial systems, minimization algorithms will find a
 local minimum rather than the global minimum.
@@ -1135,7 +1135,7 @@ \subsubsection{Improving the script}
 \caption{a)~Evolution of the numbers $N_\text{1, in}$ and $N_\text{2, in}$ of atoms
 of types 1 and 2, respectively, within the \lmpcmd{cyl\_in} region as functions
 of time $t$.  b)~Evolution of the coordination number $C_{1-2}$ (compute \lmpcmd{sumcoor12})
-between atoms of types 1 and 2.} 
+between atoms of types 1 and 2.}
 \label{fig:mixing}
 \end{figure}
 
@@ -1699,7 +1699,7 @@ \subsubsection{Breakable bonds}
 bonds break, the energy relaxes abruptly, as can be seen near $t=32~\text{ps}$ in Fig.~\ref{fig:CNT-breakable-energy-stress}\,a.
 Using a similar script as previously,
 i.e.,~\href{\filepath tutorial2/unbreakable-yaml-reader.py}{\dwlcmd{unbreakable-yaml-reader.py}},
-import the data into Python and generate the stress-strain curve (Fig.~\ref{fig:CNT-breakable-energy-stress}\,b).  The 
+import the data into Python and generate the stress-strain curve (Fig.~\ref{fig:CNT-breakable-energy-stress}\,b).  The
 stress-strain curve reveals a linear (elastic) regime where $F_\text{cnt} \propto \Delta L_\text{cnt}$
 for $\Delta L_\text{cnt} < 5\,\%$, and a non-linear (plastic) regime
 for $5\,\% < \Delta L_\text{cnt} < 25\,\%$.
@@ -2129,7 +2129,7 @@ \subsubsection{Stretching the PEG molecule}
 dump mydmp all local 100 pull.dat index c_dphi c_prop
 \end{lstlisting}
 By contrast with the radius of gyration (compute \lmpcmd{rgyr}), the dihedral angle  % SG: why is c_prop not printed?
-$\phi$ (compute \lmpcmd{dphi}) is returned as a vector by the \lmpcmd{compute dihedral/local} 
+$\phi$ (compute \lmpcmd{dphi}) is returned as a vector by the \lmpcmd{compute dihedral/local}
 command and must be written to a file using the \lmpcmd{dump local} command.
 
 Finally, let us simulate 15 picoseconds without any external force:
@@ -2768,7 +2768,7 @@ \subsubsection{Imposed shearing}
 the average force on each wall is given by \lmpcmd{f\_mysf1[1]} and \lmpcmd{f\_mysf2[1]}
 and is approximately $2.7\,\mathrm{kcal/mol/\AA}$ in magnitude.  Using a surface area
 for the walls of $A = 6 \cdot 10^{-18}\,\text{m}^2$, one obtains an estimate for
-the shear viscosity for the confined fluid of $\eta = 3.1\,\text{mPa.s}$ using Eq.~\eqref{eq:eta}. 
+the shear viscosity for the confined fluid of $\eta = 3.1\,\text{mPa.s}$ using Eq.~\eqref{eq:eta}.
 
 \begin{note}
 The viscosity calculated at such a high shear rate may differ from the expected
@@ -4008,7 +4008,7 @@ \subsection{Tutorial 8: Reactive Molecular Dynamics}
 
 \begin{figure}
 \centering
-\includegraphics[width=0.7\linewidth]{REACT.png}
+\includegraphics[width=\linewidth]{REACT.png}
 \caption{Initial configuration for \hyperref[bond-react-label]{Tutorial 8}.
 The system consists of 200 styrene molecules packed around a single-walled
 CNT, with a mass density for the whole system of $0.9~\text{g/cm}^3$.}
@@ -4039,7 +4039,7 @@ \subsubsection{Creating the system}
 The \textit{class2} bond, angle, dihedral, and improper styles are used as
 well, see the documentation for a description of their respective potentials.
 The \lmpcmd{mix sixthpower} imposes the following mixing rule for the calculation
-of the cross coefficients: 
+of the cross coefficients:
 \begin{eqnarray}
 \nonumber
 \sigma_{ij} & = & 2^{-1/6} (\sigma^6_i+\sigma_j^6)^{1/6}, ~ \text{and} \\
@@ -4073,7 +4073,7 @@ \subsubsection{Creating the system}
 by manually shrinking the simulation box at a constant rate.  The dimension parallel
 to the CNT axis is maintained fixed because the CNT is periodic in that direction.
 Add the following commands to \flecmd{mixing.lmp}:
-% SG: I removed the loop local, unless its important? But if it is, we have to 
+% SG: I removed the loop local, unless its important? But if it is, we have to
 % explain what it does and why it was chosen here.
 \begin{lstlisting}
 velocity all create 530 9845 dist gaussian rot yes
@@ -4089,7 +4089,7 @@ \subsubsection{Creating the system}
 run 9000
 \end{lstlisting}
 The \lmpcmd{fix halt} command is used to stop the box shrinkage once the
-target density is reached. 
+target density is reached.
 
 For the next stage of the simulation, we will use \lmpcmd{dump image} to
 output images every 200 steps:
@@ -4114,7 +4114,7 @@ \subsubsection{Creating the system}
 unfix myhal
 reset_timestep 0
 
-group CNT molecule 1 2 3
+group CNT molecule 1
 fix myrec CNT recenter NULL 0 0 units box shift all
 
 run 10000
@@ -4250,9 +4250,9 @@ \subsubsection{Simulating the reaction}
 
 \begin{figure}
 \centering
-\includegraphics[width=0.7\linewidth]{REACT-final.png}
+\includegraphics[width=\linewidth]{REACT-final.png}
 \caption{Final configuration for \hyperref[bond-react-label]{Tutorial 8}.
-The atoms from the formed polymer named \lmpcmd{c1}, \lmpcmd{c2}, and 
+The atoms from the formed polymer named \lmpcmd{c1}, \lmpcmd{c2}, and
 \lmpcmd{c3} are colored in pink.}
 \label{fig:REACT-final}
 \end{figure}
@@ -4262,7 +4262,7 @@ \subsubsection{Simulating the reaction}
 to track which atoms are being stabilized and which atoms are undergoing
 dynamics with the system-wide time integrator (here, \lmpcmd{fix nvt}).
 When reaction stabilization is employed, there should not be a time integrator acting on
-the group \lmpcmd{all}.  Instead, the group of atoms not currently
+the group \mbox{\lmpcmd{all}.}  Instead, the group of atoms not currently
 undergoing stabilization is named by appending `\_REACT' to the user-provided prefix.
 \end{note}
 
@@ -4291,10 +4291,10 @@ \subsubsection{Simulating the reaction}
 \caption{a) Evolution of the system temperature, $T$,
 as a function of the time, $t$, during the polymerization step of
 \hyperref[bond-react-label]{Tutorial 8}.
-b) Evolution of the three reaction counts, corresponding respecively to
-the polymerization of two styrene monomers (Rnx~1), the  addition of a styrene
-monomer to the end of a growing polymer chain (Rnx~2), and to the linking
-of two polymer chains (Rnx~3).}
+b) Evolution of the three reaction counts, corresponding respectively to
+the polymerization of two styrene monomers (Rxn~1), the  addition of a styrene
+monomer to the end of a growing polymer chain (Rxn~2), and to the linking
+of two polymer chains (Rxn~3).}
 \label{fig:evolution-reacting}
 \end{figure}
 
