realign figures, remove some redundant text, rephrase "funny" formulations

Author: akohlmey

lammps-tutorials.tex

@@ -2468,11 +2468,11 @@ \subsubsection{System preparation}
 \end{lstlisting}
 These lines are used to define the most basic parameters, including the
 {\color{blue}atom style, the form of the non-bonded, bond and angle potentials as well as
-other specifics about the non-boned interactions}.  Here, \lmpcmd{lj/cut/tip4p/long} 
-imposes a Lennard-Jones potential with a cut-off at $12\,\text{\AA{}}$ and a long-range 
-Coulomb potential.  {\color{blue} The parameters \lmpcmd{O}, \lmpcmd{H}, \lmpcmd{O-H}, 
-and \lmpcmd{H-O-H} correspond respectively to the oxygens, hydrogens, O-H bonds, and 
-H-O-H angle constraints of the water molecules; their definitions, provided by the 
+other specifics about the non-boned interactions}.  Here, \lmpcmd{lj/cut/tip4p/long}
+imposes a Lennard-Jones potential with a cut-off at $12\,\text{\AA{}}$ and a long-range
+Coulomb potential.  {\color{blue} The parameters \lmpcmd{O}, \lmpcmd{H}, \lmpcmd{O-H},
+and \lmpcmd{H-O-H} correspond respectively to the oxygens, hydrogens, O-H bonds, and
+H-O-H angle constraints of the water molecules; their definitions, provided by the
 \lmpcmd{labelmap} commands, will be clarified below.}
 
 So far, the commands are relatively similar to those in the previous tutorial,
@@ -2618,15 +2618,17 @@ \subsubsection{System preparation}
 bond_coeff O-H 0 0.9572
 angle_coeff H-O-H 0 104.52
 \end{lstlisting}
-The \lmpcmd{bond\_coeff} command, used here for the O-H bond of the water
-molecule, sets both the spring constant of the harmonic potential and the
-equilibrium bond distance of $0.9572~\text{\AA{}}$.  The constant can be 0 for a
-rigid water molecule because the SHAKE algorithm, {\color{blue} which will be summoned
-later in the script using a command line,} will {\color{blue} fix the intramolecular
-structure} of the water {\color{blue} molecules} (see below)~\cite{ryckaert1977numerical, andersen1983rattle}.
-Similarly, the \lmpcmd{angle\_coeff} command for the H-O-H angle of the water molecule sets
-the force constant of the angular harmonic potential to 0 and the equilibrium
-angle to $104.52^\circ$.
+The \lmpcmd{bond\_coeff} command, used here for the O-H bond of the
+water molecule, sets both the spring constant of the harmonic potential
+and the equilibrium bond distance of $0.9572~\text{\AA{}}$.  The force
+constant can be 0 for a rigid water molecule because the SHAKE
+algorithm, {\color{blue} which will be used in the input at a later
+  step,} will {\color{blue} constrain the intramolecular structure} of
+the water {\color{blue} molecules} (see
+below)~\cite{ryckaert1977numerical, andersen1983rattle}.  Similarly, the
+\lmpcmd{angle\_coeff} command for the H-O-H angle of the water molecule
+sets the force constant of the angular harmonic potential to 0 and the
+equilibrium angle to $104.52^\circ$.
 
 Alongside \flecmd{parameters.inc}, the \flecmd{groups.inc} file contains
 several \lmpcmd{group} commands to \textcolor{blue}{define groups of atoms based
@@ -3105,7 +3107,7 @@ \subsubsection{Prepare and relax}
 and a \lmpcmd{.data} file is imported by the \lmpcmd{read\_data} command.
 
 The initial topology given by \href{\filepath tutorial5/silica.data}{\dwlcmd{silica.data}}
-{\color{blue} corresponds to} a small amorphous silica structure.  
+{\color{blue} corresponds to} a small amorphous silica structure.
 {\color{blue}This structure was generated in a prior
 simulation using the Vashishta force field~\cite{vashishta1990interaction}.}
 If you open the \flecmd{silica.data} file, you will find in the \lmpcmd{Atoms}
@@ -3125,7 +3127,7 @@ \subsubsection{Prepare and relax}
 pair_coeff * * ffield.reax.CHOFe Si O
 fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
 \end{lstlisting}
-In this case, the \lmpcmd{pair\_style reaxff} is used without a control file 
+In this case, the \lmpcmd{pair\_style reaxff} is used without a control file
 {\color{blue}(see note below)}.  The
 \lmpcmd{safezone} and \lmpcmd{mincap} keywords are added to prevent
 allocation issues, which sometimes can trigger segmentation faults and
@@ -3159,7 +3161,7 @@ \subsubsection{Prepare and relax}
 variable vq atom q
 \end{lstlisting}
 {\color{blue} The definition of the equal style variables qSi and qO
-make use of functions pre-defined within LAMMPS that allow calculating 
+make use of functions pre-defined within LAMMPS that allow calculating
 the total charge of atoms belonging to a group (charge()) and the total
 number of atoms in the group (count()).  }
 To print the averaged charges \lmpcmd{qSi} and \lmpcmd{qO} using the
@@ -3445,7 +3447,7 @@ \subsubsection{Decorate the surface}
 fix myspec all reaxff/species 5 1 5 decorate.species &
   element Si O H
 \end{lstlisting}
-{\color{blue} The commands above are, once again, similar to the ones of the previous script.}  
+{\color{blue} The commands above are, once again, similar to the ones of the previous script.}
 Here, the $+1 \mathrm{e}{-10}$ was added to the denominator of the \lmpcmd{variable qH}
 to avoid dividing by 0 at the beginning of the simulation{\color{blue}, as no hydrogen
 atoms exists in the simulation domain yet}.  Finally, let us
@@ -3529,7 +3531,7 @@ \subsubsection{Generation of the silica block}
 create_atoms Si random 240 5802 box overlap 2.0 maxtry 500
 create_atoms O random 480 1072 box overlap 2.0 maxtry 500
 \end{lstlisting}
-{\color{blue}In line with what is done in previous tutorials, the} 
+{\color{blue}In line with what is done in previous tutorials, the}
 \lmpcmd{create\_atoms} commands are used to place
 240 Si atoms and 480 O atoms, respectively.  This corresponds to
 an initial density of approximately $2$\,g/cm$^3$, which is close
@@ -3585,9 +3587,9 @@ \subsubsection{Generation of the silica block}
 fix mynvt all nvt temp 6000 300 0.1
 run 30000
 \end{lstlisting}
-{\color{blue} In this case, the initial and final target temperatures 
+{\color{blue} In this case, the initial and final target temperatures
 set for the Nose-Hoover thermostat is different, causing it to evolve
-linearly within the number of timesteps evoked in the \lmpcmd{run} 
+linearly within the number of timesteps evoked in the \lmpcmd{run}
 command.  }
 In the third step, the system is equilibrated at the final desired
 conditions, $T = 300\,\text{K}$ and $p = 1\,\text{atm}$,
@@ -3601,7 +3603,7 @@ \subsubsection{Generation of the silica block}
 write_data generate.data
 \end{lstlisting}
 Here, an anisotropic barostat is used.
-{\color{blue}As previously mentioned, a}nisotropic 
+{\color{blue}As previously mentioned, a}nisotropic
 barostats adjust the dimensions independently, which is
 generally suitable for a solid phase.
 
@@ -3611,7 +3613,7 @@ \subsubsection{Generation of the silica block}
 {\color{blue}is deforming} during the last stage of the simulation
 (Fig.~\ref{fig:GCMC-dimension}\,b).  After the simulation completes, the final
 {\color{blue} microstate attained during the dynamics and the system topology
-will be written to a} LAMMPS {\color{blue} data }file called \flecmd{generate.data} 
+will be written to a} LAMMPS {\color{blue} data }file called \flecmd{generate.data}
 {\color{blue}which} will be located next to \flecmd{generate.lmp} (Fig.~\ref{fig:GCMC-snapshot}).
 
 \begin{figure}
@@ -3647,7 +3649,6 @@ \subsubsection{Cracking the silica}
 thermo 250
 thermo_style custom step temp etotal vol density
 \end{lstlisting}
-
 Let us progressively increase the size of the box in the $x$ direction,
 forcing the silica to deform and eventually crack.  To achive this,
 the \lmpcmd{fix deform} command is used, with a rate
@@ -3662,8 +3663,7 @@ \subsubsection{Cracking the silica}
 write_data cracking.data
 \end{lstlisting}
 {\color{blue}As discussed, the \lmpcmd{fix nvt} command integrates the Nosé-Hoover equations
-of motion as originally derived to sample the NVT ensemble, 
-which allows controlling the temperature of the system.}
+of motion to sample the NVT ensemble, which allows controlling the temperature of the system.}
 As observed from the generated images, the atoms
 progressively adjust to the changing box dimensions.  At some point,
 bonds begin to break, leading to the appearance of
@@ -3688,13 +3688,13 @@ \subsubsection{Adding water}
 
 To add the water molecules to the silica, we will employ the Monte Carlo
 method in the grand canonical ensemble (GCMC).  In short, the system is
-placed into contact with a virtual reservoir {\color{blue} containing pure 
-water at a given thermodynamic state}, and multiple attempts to insert 
-water molecules at random positions are made.  {\color{blue} In the grand 
-canonical ensemble, each} attempt is either accepted or rejected based on 
-{\color{blue} internal} energy {\color{blue} and chemical potential, $\mu$} 
+placed into contact with a virtual reservoir {\color{blue} containing pure
+water at a given thermodynamic state}, and multiple attempts to insert
+water molecules at random positions are made.  {\color{blue} In the grand
+canonical ensemble, each} attempt is either accepted or rejected based on
+{\color{blue} internal} energy {\color{blue} and chemical potential, $\mu$}
 considerations.  For further details, please refer to
-classical textbooks like Ref.~\citenum{frenkel2023understanding}. 
+classical textbooks like Ref.~\citenum{frenkel2023understanding}.
 
 % \paragraph{Using hydrid potentials}
 
@@ -3706,11 +3706,11 @@ \subsubsection{Adding water}
 % $\text{SiO}_2$), and TIP4P (for water).  Here, the TIP4P/2005 model is
 % employed for the water~\cite{abascal2005general}.  Open the
 % \flecmd{gcmc.lmp} file, which should contain the following lines:
-For this next step, we need to {\color{blue} specify the force field used 
+For this next step, we need to {\color{blue} specify the force field used
 to model the interactions in the system}. The TIP4P/2005 model is employed
 for the water~\cite{abascal2005general}, while no {\color{blue} interaction
-within silica is defined, as it will be seen farther below}. 
-{\color{blue} This is because the} atoms of the silica will 
+within silica is defined, as it will be seen farther below}.
+{\color{blue} This is because the} atoms of the silica will
 remain frozen during this part {\color{blue}of the simulation}.
 Only the cross-interactions between water and silica need
 to be defined. Open the \flecmd{gcmc.lmp} file, which should contain the following lines:
@@ -3731,7 +3731,7 @@ \subsubsection{Adding water}
 The PPPM solver~\cite{luty1996calculating} is specified with the \lmpcmd{kspace}
 command, and is used to compute the long-range Coulomb interactions associated
 with \lmpcmd{tip4p/long}.  Finally, the {\color{blue} form of} the bond
-and angle{\color{blue} potentials} of the water molecules are defined; however, 
+and angle{\color{blue} potentials} of the water molecules are defined; however,
 {\color{blue} as previously discussed,} these specifications are
 not critical since TIP4P/2005 is a rigid water model.}
 
@@ -3812,7 +3812,7 @@ \subsubsection{Adding water}
 file, the \lmpcmd{create\_atoms} command is used to include three water molecules
 in the system.  Then, add the following \lmpcmd{pair\_coeff} (and
 \lmpcmd{bond\_coeff} and \lmpcmd{angle\_coeff}) commands
-to \flecmd{gcmc.lmp} {\color{blue}in order to specify the potential parameters}:
+to \flecmd{gcmc.lmp} {\color{blue}in order to set the potential parameters}:
 \begin{lstlisting}
 pair_coeff * * 0 0
 pair_coeff Si OW 0.0057 4.42
@@ -3825,8 +3825,8 @@ \subsubsection{Adding water}
 % The force field Vashishta applies only to \lmpcmd{Si} and \lmpcmd{O} of $\text{SiO}_2$,
 % and not to the \lmpcmd{OW} and \lmpcmd{HW} of $\text{H}_2\text{O}$, thanks to the \lmpcmd{NULL} parameters
 % used for atoms of types \lmpcmd{OW} and \lmpcmd{HW}.
-Pair coefficients for the {\color{blue}potentials underlying the} \lmpcmd{lj/cut/tip4p/long} 
-{\color{blue}style} are defined between O($\text{H}_2\text{O}$) and between H($\text{H}_2\text{O}$)
+Pair coefficients for the \lmpcmd{lj/cut/tip4p/long} {\color{blue}pair style} are
+defined between O($\text{H}_2\text{O}$) and between H($\text{H}_2\text{O}$)
 atoms, as well as between O($\text{SiO}_2$)-O($\text{H}_2\text{O}$) and
 Si($\text{SiO}_2$)-O($\text{H}_2\text{O}$).  Thus, the fluid-fluid and the
 fluid-solid interactions will be adressed with by the \lmpcmd{lj/cut/tip4p/long} potential.
@@ -4116,7 +4116,7 @@ \subsubsection{Method 1: Free sampling}
 fix myadf all addforce v_F 0.0 0.0 energy v_U
 \end{lstlisting}
 Next, we {\color{blue}use the Newtonian equations of motion with a
-Langevin thermostat by combining }the \lmpcmd{fix nve} with a 
+Langevin thermostat by combining }the \lmpcmd{fix nve} with a
 \lmpcmd{fix langevin} {\color{blue}command}:
 \begin{lstlisting}
 fix mynve all nve
@@ -4128,7 +4128,7 @@ \subsubsection{Method 1: Free sampling}
 fluctuates around a target value.
 % SG: may be discuss the choice of constant "500" -> chosen for a relatiely weak coupling with thermostat (add a box?)
 % CA: I can propose something that can be put in a yellow box. Feel free to uncomment the lines below and modify it if you want to.
-% {\color{blue}You can find proposed in the LAMMPS documentation  
+% {\color{blue}You can find proposed in the LAMMPS documentation
 % values of 100x and 1000x the value of the timestep for the damping
 % constants of the thermostats and barostats. Here, a smaller
 % value is used in order to have the temperature of the system
@@ -4147,7 +4147,7 @@ \subsubsection{Method 1: Free sampling}
 
 To ensure that the equilibration time is sufficient, we will track the evolution of
 the number of atoms in the central - energetically unfavorable - region,
-{\color{blue} defined below under the name} \lmpcmd{mymes}, using 
+{\color{blue} defined below under the name} \lmpcmd{mymes}, using
 the \lmpcmd{n\_center} variable:
 \begin{lstlisting}
 region mymes block -${x0} ${x0} INF INF INF INF
@@ -4161,7 +4161,7 @@ \subsubsection{Method 1: Free sampling}
 dump_modify viz backcolor white acolor 1 cyan &
     adiam 1 3 boxcolor black
 \end{lstlisting}
-A \lmpcmd{dump image} command was also added for system visualization.  
+A \lmpcmd{dump image} command was also added for system visualization.
 {\color{blue} The other commands should also be familiar from previous tutorials.}
 
 Finally, let us perform an equilibration of 50000 steps,
@@ -4328,7 +4328,7 @@ \subsubsection{Method 2: Umbrella sampling}
 \end{lstlisting}
 
 So far, our code resembles that of Method 1, except for the additional particle
-of type 2.  Particles of types 1 and 2 are identical.  
+of type 2.  Particles of types 1 and 2 are identical.
 However, the particle of type 2 will also
 be exposed to the biasing potential $V$, which forces it to explore the
 central part of the box (Fig.~\ref{fig:US-system-biased}), {\color{blue} thus
@@ -4366,9 +4366,9 @@ \subsubsection{Method 2: Umbrella sampling}
 jump SELF loop
 \end{lstlisting}
 {\color{blue} The definition of a variable of loop style serves the same purpose
-as in (\hyperref[reactive-silicon-dioxide-label]{Tutorial 5}), and we highlight 
+as in (\hyperref[reactive-silicon-dioxide-label]{Tutorial 5}), and we highlight
 here the particular utility of using its value
-to distinguish the files written by the \lmpcmd{fix ave_/time} command for the
+to distinguish the files written by the \lmpcmd{fix ave\_time} command for the
 different bias potentials.}
 The \lmpcmd{spring} command imposes the additional harmonic potential $V$ with
 the previously defined spring constant $k$ {\color{blue}to the atoms in the group \lmpcmd{topull}}.  The center of the harmonic
@@ -4476,8 +4476,8 @@ \subsubsection{Creating the system}
 \end{lstlisting}
 The \lmpcmd{class2} styles compute a 6/9 Lennard-Jones potential~\cite{sun1998compass}.
 The \textit{class2} bond, angle, dihedral, and improper styles are used as
-well, see the documentation for a description of the respective {\color{blue} potential 
-form they, each, prescribe}.  
+well, see the documentation for a description of the respective {\color{blue} potential
+form they, each, prescribe}.
 {\color{blue}The \lmpcmd{tail yes} option adds long-range van der Waals tail
 corrections to the energy and pressure.}
 The \lmpcmd{mix sixthpower} imposes the following mixing rule for the calculation
@@ -4510,10 +4510,10 @@ \subsubsection{Creating the system}
 minimize 1.0e-4 1.0e-6 100 1000
 reset_timestep 0
 \end{lstlisting}
-{\color{blue}These commands should be familiar from previous tutorials.}  
+{\color{blue}These commands should be familiar from previous tutorials.}
 
 Then, let us densify the system to a target value of $0.9~\text{g/cm}^3$
-by {\color{blue}imposing the} shrinking {\color{blue}of} the simulation box at a constant rate.  
+by {\color{blue}imposing the} shrinking {\color{blue}of} 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
@@ -4565,7 +4565,7 @@ \subsubsection{Creating the system}
 
 write_data mixing.data
 \end{lstlisting}
-For visualization purposes, the atoms {\color{blue} of} 
+For visualization purposes, the atoms {\color{blue} of}
 the CNT \lmpcmd{group} {\color{blue}are} moved
 to the center of the box using \lmpcmd{fix recenter}.
 As the time progresses, the system density,
@@ -4704,25 +4704,18 @@ \subsubsection{Simulating the reaction}
 % as I literally just figured it out to write them. (PS: I just realized that some
 % of it may be redundant with the note, but I would still leave it as the reader
 % will have the full information.
-With the \lmpcmd{stabilization} keyword, the \lmpcmd{bond/react} command will
+With the \lmpcmd{stabilization} keyword, the \lmpcmd{fix bond/react} command will
 stabilize the atoms involved in the reaction using the \lmpcmd{nve/limit}
-command with a maximum displacement of $0.03\,\mathrm{\AA{}}$.  
-{\color{blue}The \lmpcmd{nve/limit} is a command that functions similar to the
-\lmpcmd{nve} in terms of equation of motion implied, but has a constraint on
-how close atoms will be. In this case, it will be summoned internally within
-LAMMS as the \lmpcmd{bond/react} appears.}  
+command with a maximum displacement of $0.03\,\mathrm{\AA{}}$.
+{\color{blue}The \lmpcmd{fix nve/limit} command functions similar to
+\lmpcmd{fix nve}, but restricts how far atoms can move in a single time step, even with
+very large forces.}
 By default, each reaction is stabilized for 60 time steps.  Each \lmpcmd{react} keyword
 corresponds to a reaction, e.g.,~a transformation of \lmpcmd{mol1} into \lmpcmd{mol2}
 based on the atom map \lmpcmd{M-M.rxnmap}.  Implementation details about each reaction,
 such as the reaction distance cutoffs and the frequency with which to search for
 reaction sites, are also specified in this command.
 
-\begin{note}
-{\color{blue}The \lmpcmd{fix nve/limit} integrates command Newton's equations of motion
-while limiting the maximum displacement of atoms per timestep.  This is
-useful for preventing atoms from moving too far due to large forces.}
-\end{note}
-
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{REACT-final.png}
@@ -4741,7 +4734,7 @@ \subsubsection{Simulating the reaction}
 undergoing stabilization is named by appending `\_REACT' to the user-provided prefix.
 \end{note}
 
-Add the following commands to \flecmd{polymerize.lmp} to 
+Add the following commands to \flecmd{polymerize.lmp} to
 {\color{blue} carry out the dynamics using a Nosé-Hoover thermostat}
 while ensuring that the CNT remains centered in the simulation box:
 \begin{lstlisting}