some tests with the breakable cnt part

Author: simongravelle

files/tutorial2/breakable.lmp

@@ -6,4 +6,30 @@ read_data breakable.data
 pair_style airebo 3.0
 pair_coeff * * CH.airebo C
 
+group carbon_atoms type 1
+
+variable xmax equal bound(carbon_atoms,xmax)-0.5
+variable xmin equal bound(carbon_atoms,xmin)+0.5
+region rtop block ${xmax} INF INF INF INF INF
+region rbot block INF ${xmin} INF INF INF INF
+region rmid block ${xmin} ${xmax} INF INF INF INF
+
+group cnt_top region rtop
+group cnt_bot region rbot
+group cnt_mid region rmid
+
+variable xmax_del equal ${xmax}-2
+variable xmin_del equal ${xmin}+2
+region rdel block ${xmin_del} ${xmax_del} INF INF INF INF
+
+group rdel region rdel
+delete_atoms random fraction 0.02 no rdel NULL 482793
+
+reset_atoms id sort yes
+velocity cnt_mid create ${T} 48455 mom yes rot yes
+fix mynve all nve
+compute Tmid cnt_mid temp
+fix myber cnt_mid temp/berendsen ${T} ${T} 0.1
+fix_modify myber temp Tmid
+
 run 0 post no

files/tutorial2/solution/CH.airebo

@@ -0,0 +1 @@
+../CH.airebo

files/tutorial2/solution/breakable.lmp

@@ -0,0 +1,56 @@
+units metal
+atom_style atomic
+boundary f f f
+
+read_data breakable.data
+pair_style airebo 3.0
+pair_coeff * * CH.airebo C
+
+group carbon_atoms type 1
+
+variable xmax equal bound(carbon_atoms,xmax)-0.5
+variable xmin equal bound(carbon_atoms,xmin)+0.5
+region rtop block ${xmax} INF INF INF INF INF
+region rbot block INF ${xmin} INF INF INF INF
+region rmid block ${xmin} ${xmax} INF INF INF INF
+
+group cnt_top region rtop
+group cnt_bot region rbot
+group cnt_mid region rmid
+
+variable xmax_del equal ${xmax}-2
+variable xmin_del equal ${xmin}+2
+region rdel block ${xmin_del} ${xmax_del} INF INF INF INF
+
+group rdel region rdel
+delete_atoms random fraction 0.02 no rdel NULL 482793
+
+reset_atoms id sort yes
+velocity cnt_mid create 300 48455 mom yes rot yes
+
+fix mynve1 cnt_top nve
+fix mynve2 cnt_bot nve
+fix mynvt cnt_mid nvt temp 300 300 1.0
+fix mysf1 cnt_bot setforce 0 0 0
+fix mysf2 cnt_top setforce 0 0 0
+
+velocity cnt_bot set 0 0 0
+velocity cnt_top set 0 0 0
+
+variable L equal xcm(cnt_top,x)−xcm(cnt_bot,x)
+variable F equal f_mysf1[1]−f_mysf2[1]
+
+dump mydmp all image 500 dump.*.ppm type type adiam 1.5 box no 0.01 view 0 90 zoom 1.8 shiny 0.1 fsaa yes
+dump_modify mydmp pad 5 backcolor white acolor 1 pink
+
+compute Tmid cnt_mid temp
+thermo 100
+thermo_style custom step temp etotal v_L v_F
+thermo_modify temp Tmid line yaml
+
+timestep 0.0005
+run 10000
+
+velocity cnt_top set 0.75 0 0
+velocity cnt_bot set -0.75 0 0
+run 30000 

lammps-tutorials.tex

@@ -1609,7 +1609,7 @@ \subsubsection{Breakable bonds}
 
 \paragraph{Adapt the topology file}
 
-Since bonds,angles, and dihedrals do not need to be
+Since bonds, angles, and dihedrals do not need to be
 explicitly set when using AIREBO, some simplification must be made to the
 \flecmd{.data} file. The new \flecmd{.data}
 file is named \href{\filepath tutorial2/breakable.data}{\dwlcmd{breakable.data}},
@@ -1618,20 +1618,9 @@ \subsubsection{Breakable bonds}
 required for placing the atoms in the box, but no bond/angle/dihedral information.
 Another difference between the \flecmd{unbreakable.data} and \flecmd{breakable.data} files
 is that, here, a larger distance of 120~Ångströms was used for the box size along
-the $x$ axis, to allow for larger deformation.
+the $x$ axis, to allow for larger deformation of the CNT.
 
-\paragraph{Use of AIREBO potential}
-
-Then, let us import the LAMMPS data file, and set the pair coefficients by adding
-the following lines into \flecmd{input.lmp}:
-\begin{lstlisting}
-# System definition
-read_data cnt_atom.data
-pair_coeff * * CH.airebo C
-\end{lstlisting}
-Here, there is one atom type, which we impose to be `carbon' by using
-the letter \textit{C}. Download the \href{\filepath tutorial2/breakable-bonds/CH.airebo}{\dwlcmd{CH.airebo}}
-file and place it within the \textit{breakable-bonds/} folder. The rest of the
+The rest of the
 \flecmd{input.lmp} is very similar to the previous one:
 
 \begin{lstlisting}