cleaned tutorial 6

Author: simongravelle

files/tutorial6/generate.lmp

@@ -0,0 +1,7 @@
+
+units metal
+boundary p p p
+atom_style full
+pair_style vashishta
+neighbor 1.0 bin
+neigh_modify delay 1

files/tutorial6/solution/generate.lmp

@@ -17,7 +17,7 @@ dump_modify mydmp backcolor white &
   acolor Si yellow adiam Si 2.5 &
   acolor O red adiam O 2
 
-thermo 1000
+thermo 500
 thermo_style custom step temp etotal vol lx ly lz
 
 velocity all create 6000 4928459 rot yes dist gaussian

lammps-tutorials.tex

@@ -2745,7 +2745,7 @@ \subsubsection{Prepare and relax}
 
 The first action we need to perform here is to relax the structure with ReaxFF,
 which we are gonna do using molecular dynamics.  As always, to make sure that the system
-equilibrates nicely, we will us track certain parameters over time. To set up this
+equilibrates nicely, we will us track certain parameters over time.  To set up this
 tutorial, select \guicmd{Start Tutorial 5} from the
 \guicmd{Tutorials} menu of LAMMPS--GUI and follow the instructions.
 The editor should display the following content corresponding to \flecmd{relax.lmp}:
@@ -3100,32 +3100,24 @@ \subsection{Tutorial 6: Water adsorption in silica}
 \centering
 \includegraphics[width=0.55\linewidth]{GCMC}
 \caption{Water molecules adsorbed in cracked silica (SiO$_2$) material as simulated
-during \hyperref[gcmc-silica-label]{Tutorial 6}. Water molecules are colored in
+during \hyperref[gcmc-silica-label]{Tutorial 6}.  Water molecules are colored in
 cyan and white, oxygen (O) atoms from SiO$_2$ in red, and silicon (Si) atoms in yellow.}
 \label{fig:GCMC}
 \end{figure}
 
 \noindent The objective of this tutorial is to combine molecular dynamics and
 grand canonical Monte Carlo simulations to compute the adsorption of water
-molecules in cracked silica material (Fig.\,\ref{fig:GCMC}). This tutorial
+molecules in cracked silica material (Fig.\,\ref{fig:GCMC}).  This tutorial
 illustrates the use of the grand canonical ensemble in molecular simulation, an
-open ensemble in which the number of atoms or molecules within the simulation
-box is not constant. When using the grand canonical ensemble, it is possible to
-impose the chemical potential (or pressure) of a given fluid in a nanoporous structure.
+open ensemble where the number of atoms or molecules in the simulation box can vary.
+By employing the grand canonical ensemble, we will set the chemical
+potential of water within a nanoporous SiO$_2$ structure.
 
 \subsubsection{Generation of the silica block}
-\noindent Let us first generate a block of amorphous silica ($\text{SiO}_2$).
-To do so, we are going to replicate a building block containing 3 Si and 6 O atoms.
-Create two folders side by side, and name them respectively \flrcmd{Potential/}
-and \flrcmd{SilicaBlock/}. The initial data file for the SiO atoms called
-\href{\filepath tutorial6/SiO.data}{\dwlcmd{SiO.data}}
-must be downloaded and saved in \flrcmd{SilicaBlock/}. This data file contains
-the coordinates of the 9 atoms, their masses, and their charges.
 
-Let us replicate these atoms using LAMMPS, and apply an annealing procedure to
-obtain a block of amorphous silica. Create a new input file called \flecmd{input.lmp}
-in the \flrcmd{SilicaBlock/} folder, and copy
-the following lines into it:
+\noindent To begin this tutorial, select \guicmd{Start Tutorial 6} from the
+\guicmd{Tutorials} menu of LAMMPS--GUI and follow the instructions.
+The editor should display the following content corresponding to \flecmd{generate.lmp}:
 \begin{lstlisting}
 units metal
 boundary p p p
@@ -3134,85 +3126,86 @@ \subsubsection{Generation of the silica block}
 neighbor 1.0 bin
 neigh_modify delay 1
 \end{lstlisting}
-The main difference from some of the previous tutorials is the use of the \textit{Vashishta}
-pair style. The Vashishta potential is a bond-angle energy-based potential, it deduces
-the bonds between atoms from their relative positions \cite{vashishta1990interaction}.
+The main difference from some of the previous tutorials is the use of the \lmpcmd{Vashishta}
+pair style. The Vashishta potential is a bond-angle energy-based potential, which
+determines the bonds between atoms from their relative positions \cite{vashishta1990interaction}.
 
-Let us then import the system consisting of 9 atoms, and replicate it four times
-in all three directions of space, thus creating a system with 576 atoms. Add the
-following lines into \flecmd{input.lmp}:
+The initial data file for the SiO atoms called
+\href{\filepath tutorial6/SiO.data}{\dwlcmd{SiO.data}}
+must be downloaded next to \flecmd{generate.lmp}.  This data file contains
+the coordinates of 9 atoms, their masses, and their charges. Let us replicate
+these 9 atoms using LAMMPS, and apply an annealing procedure to
+obtain a block of amorphous silica.
+
+Next, import \flecmd{SiO.data} and replicate it
+in all three directions of space.  Add the
+following lines to \flecmd{generate.lmp}:
 \begin{lstlisting}
 read_data SiO.data
-replicate 4 4 4
+replicate 5 4 4
 \end{lstlisting}
-Then, let us specify the pair coefficients by indicating that the first atom type
-is \textit{Si} and the second is \textit{O}. Let us also add a dump command to
-print out the positions of the atoms every 5000 steps:
+Now, specify the pair coefficients by indicating that the first atom type
+is \lmpcmd{Si} and the second is \lmpcmd{O}:
 \begin{lstlisting}
-pair_coeff * * &
-    ../Potential/SiO.1990.vashishta Si O
+pair_coeff * * SiO.1990.vashishta Si O
 \end{lstlisting}
-Download the \href{\filepath tutorial6/SiO.1990.vashishta}{\dwlcmd{SiO.1990.vashishta}},
-and copy it within the \flrcmd{Potential/} folder.
+Ensure that the \href{\filepath tutorial6/SiO.1990.vashishta}{\dwlcmd{SiO.1990.vashishta}}
+file is located in the same directory as \flecmd{generate.lmp}.
 
-Let us add a \textit{dump image} command to \flecmd{input.lmp} to follow the
+Next, add a \lmpcmd{dump image} command to \flecmd{generate.lmp} to follow the
 evolution of the system with time:
 \begin{lstlisting}
-dump mydmp all image 200 dump.*.jpg type type &
-    shiny 0.1 box no 0.01 view 0 0 zoom 1.2
-dump_modify mydmp backcolor white &
-    acolor Si yellow adiam Si 2.5 &
-    acolor O red adiam O 2
-thermo 1000
-thermo_style custom step temp etotal &
-    vol lx ly lz
+dump mydmp all image 200 myimage-*.ppm type type &
+  shiny 0.1 box no 0.01 view 180 90 zoom 1.2 size 1000 650
+dump_modify mydmp backcolor white acolor Si yellow &
+  adiam Si 2.5 acolor O red adiam O 2
+\end{lstlisting}
+Additionally, let us also print the box dimensions, \lmpcmd{lx}, \lmpcmd{ly}, and \lmpcmd{lz}:
+\begin{lstlisting}
+thermo 500
+thermo_style custom step temp etotal vol lx ly lz  
 \end{lstlisting}
-Thanks to the \textit{thermo\_style custom} command, the box size along each direction
-will be printed in the log file.
 
-Finally, let us create the last part of our script. The annealing procedure is
-made of four consecutive runs. First, a $50\,\text{ps}$ phase at $T = 6000\,\text{K}$
+Finally, let us implement the annealing procedure which is
+made of four consecutive runs.  First, a $25\,\text{ps}$ phase at $T = 6000\,\text{K}$
 and isotropic pressure coupling with desired pressure $p = 100\,\text{atm}$:
 \begin{lstlisting}
-velocity all create 6000 4928459 &
-    rot yes dist gaussian
-fix npt1 all npt temp 6000 6000 0.1 &
-    iso 100 100 1
+velocity all create 6000 4928459 rot yes dist gaussian
+fix npt1 all npt temp 6000 6000 0.1 iso 100 100 1
 timestep 0.001
-run 50000
+run 25000
 \end{lstlisting}
 Then, a second phase during which the system is cooled down from $T = 6000\,\text{K}$
-to $T = 4000\,\text{K}$. An anisotropic pressure coupling is used, allowing all
+to $T = 4000\,\text{K}$.  An anisotropic pressure coupling is used, allowing all
 three dimensions of the box to evolve independently from one another:
 \begin{lstlisting}
-fix npt1 all npt temp 6000 4000 0.1 &
-    aniso 100 100 1
-run 50000
+fix npt1 all npt temp 6000 4000 0.1 aniso 100 100 1
+run 25000
 \end{lstlisting}
-Then, let us cool down the system further while also reducing the pressure, and then
-perform a small equilibration step at the final desired condition, $T = 300\,\text{K}$ and $p = 1\,\text{atm}$.
+In the third step, the system is cooled further while also reducing the
+pressure.  The final step is a short equilibration at the final desired
+condition, $T = 300\,\text{K}$ and $p = 1\,\text{atm}$:
 \begin{lstlisting}
-fix npt1 all npt temp 4000 300 0.1 &
-    aniso 100 1 1
-run 200000
-fix npt1 all npt temp 300 300 0.1 &
-    aniso 1 1 1
+fix npt1 all npt temp 4000 300 0.1 aniso 100 1 1
 run 50000
-write_data amorphousSiO.data
+fix npt1 all npt temp 300 300 0.1 aniso 1 1 1
+run 25000
+
+write_data generate.data
 \end{lstlisting}
 Here, an isotropic barostat is used for the melted phase at $T = 6000\,\text{K}$,
-and an anisotropic barostat is used for all following phases. With the anisotropic
-barostat, all three directions of space are adjusted independently from one another.
-An anisotropic barostat is usually a better choice for a solid phase. For a liquid
-or a gas, an isotropic barostat is usually the best choice.
-
-Run the simulation using LAMMPS. From the \textit{Charts} window, the temperature
-can be seen to follow well the desired annealing procedure (Fig.\,\ref{fig:GCMC-temperature}).
-The evolution of the box dimensions over time confirms that the box was indeed
-deformed isotropically during the first stage of the simulation, and then anisotropically
-(Fig.\,\ref{fig:GCMC-dimension}). After running
-the simulation, the final LAMMPS topology file called \flecmd{amorphousSiO.data}
-will be located in \flrcmd{SilicaBlock/} (Fig.\,\ref{fig:GCMC-snapshot}).
+and an anisotropic barostat is used for all following phases.  
+The anisotropic barostat adjusts the dimensions independently, which is more
+suitable for a solid phase.  For a liquid or a gas, an isotropic barostat is
+usually the best choice.
+
+Run the simulation using LAMMPS. From the \guicmd{Charts} window, the temperature
+evolution can be observed, showing that it closely follows the desired annealing procedure (Fig.\,\ref{fig:GCMC-temperature}).
+The evolution of the box dimensions over time confirms that the box
+deformed isotropically during the first stage of the simulation, followed by anisotropic deformation
+(Fig.\,\ref{fig:GCMC-dimension}).  After the simulation completes, the final
+LAMMPS topology file called \flecmd{generate.data}
+will be located next to \flecmd{generate.lmp} (Fig.\,\ref{fig:GCMC-snapshot}).
 
 \begin{figure}
 \centering