Merge pull request #22 from lammpstutorials/improve-GUI-in-tutoria3

added more GUI-compatible options in tutorial 3

Author: simongravelle

lammps-tutorials.tex

@@ -1810,15 +1810,15 @@ \subsubsection{Preparing the water reservoir}
 Create a folder called \textit{pureH2O/}. Inside this folder, create an empty text
 file called \textit{input.lmp}. Copy the following lines into it:
 {\normalsize \begin{verbatim}
-units real
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style harmonic
-pair_style lj/cut/coul/long 10
-kspace_style pppm 1e-5
-special_bonds lj 0.0 0.0 0.5 &
-    coul 0.0 0.0 1.0 angle yes
+ units real
+ atom_style full
+ bond_style harmonic
+ angle_style harmonic
+ dihedral_style harmonic
+ pair_style lj/cut/coul/long 10
+ kspace_style pppm 1e-5
+ special_bonds lj 0.0 0.0 0.5 &
+     coul 0.0 0.0 1.0 angle yes
 \end{verbatim}}
 With the unit style \textit{real}, masses are in grams per mole, distances in
 Ångstroms, time in femtoseconds, and energies in kcal/mole. With the \textit{atom\_style full}, each atom is a dot with a mass and a charge that can be linked by bonds, angles, dihedrals, and/or impropers. The \textit{bond\_style},
@@ -1837,22 +1837,22 @@ \subsubsection{Preparing the water reservoir}
 (1 for the water, 6 for the polymer), 8 angle types (1 for the water, 7 for the polymer),
 and 4 dihedral types (only for the polymer). Copy the following lines into \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-region box block -45 45 -15 15 -15 15
-create_box 8 box &
-bond/types 7 &
-angle/types 8 &
-dihedral/types 4 &
-extra/bond/per/atom 3 &
-extra/angle/per/atom 6 &
-extra/dihedral/per/atom 10 &
-extra/special/per/atom 14
+ region box block -45 45 -15 15 -15 15
+ create_box 8 box &
+ bond/types 7 &
+ angle/types 8 &
+ dihedral/types 4 &
+ extra/bond/per/atom 3 &
+ extra/angle/per/atom 6 &
+ extra/dihedral/per/atom 10 &
+ extra/special/per/atom 14
 \end{verbatim}}
 The \textit{extra/x/per/atom} commands are here for
 memory allocation. We will use a file named \textit{PARM.lmp} that contains
 all the parameters (masses, interaction energies, bond equilibrium
 distances, etc). In \textit{input.lmp}, add the following line:
 {\normalsize \begin{verbatim}
-include ../PARM.lmp
+ include ../PARM.lmp
 \end{verbatim}}
 
 Download and save the
@@ -1871,9 +1871,9 @@ \subsubsection{Preparing the water reservoir}
 \textit{H2O-SPCFw.mol} and then randomly create 1050 molecules. Add the following
 lines into \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-molecule h2omol H2O-SPCFw.mol
-create_atoms 0 random 1050 87910 NULL mol &
-    h2omol 454756 overlap 1.0 maxtry 50
+ molecule h2omol H2O-SPCFw.mol
+ create_atoms 0 random 1050 87910 NULL mol &
+     h2omol 454756 overlap 1.0 maxtry 50
 \end{verbatim}}
 The \textit{overlap 1} option of the \textit{create\_atoms} command ensures
 that no atoms are placed exactly in the same position, as this would cause the
@@ -1884,7 +1884,7 @@ \subsubsection{Preparing the water reservoir}
 of molecules. Always check the number of created atoms in the \textit{log} file
 after starting the simulation:
 {\normalsize \begin{verbatim}
-Created 3150 atoms
+ Created 3150 atoms
 \end{verbatim}}
 When LAMMPS fails to create the desired number of molecules, a WARNING appears
 in the \textit{log} file. The molecule template called
@@ -1898,9 +1898,9 @@ \subsubsection{Preparing the water reservoir}
 minimization is mandatory here given the small \textit{overlap} value of 1 Ångstrom
 chosen in the \textit{create\_atoms} command. Add the following lines into \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-group H2O type OW HW
-minimize 1.0e-4 1.0e-6 100 1000
-reset_timestep 0
+ group H2O type OW HW
+ minimize 1.0e-4 1.0e-6 100 1000
+ reset_timestep 0
 \end{verbatim}}
 In general, resetting the step of the simulation to 0 using the
 \textit{reset\_timestep} command is optional.
@@ -1911,47 +1911,47 @@ \subsubsection{Preparing the water reservoir}
 a Nosé-Hoover barostat \cite{nose1984unified, hoover1985canonical, martyna1994constant},
 by adding the following line into \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-fix mynpt all npt temp 300 300 100 &
-    iso 1 1 1000
+ fix mynpt all npt temp 300 300 100 &
+     iso 1 1 1000
 \end{verbatim}}
 The \textit{fix npt} allows us to impose both a temperature of $300\,\text{K}$
 (with a damping constant of $100\,\text{fs}$), and a pressure of 1 atmosphere
 (with a damping constant of $1000\,\text{fs}$). With the \textit{iso} keyword,
 the three dimensions of the box will be re-scaled simultaneously.
 
-Let us print the atom positions in a \textit{.lammpstrj} file every 1000 steps
-(i.e. 1 ps), print the temperature volume, and density every 100 steps in 3
-separate data files, and print the information in the terminal every 1000 steps:
+Let us output the system into images by adding the following commands to \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-dump mydmp all atom 1000 dump.lammpstrj
-variable mytemp equal temp
-variable myvol equal vol
-fix myat1 all ave/time 10 10 100 v_mytemp &
-    file temperature.dat
-fix myat2 all ave/time 10 10 100 v_myvol &
-    file volume.dat
-variable myoxy equal count(H2O)/3
-variable mydensity equal ${myoxy}/v_myvol
-fix myat3 all ave/time 10 10 100 v_mydensity &
-    file density.dat
-thermo 1000
+ dump mydmp all image 1000 dump.*.ppn type type &
+ shiny 0.1 box no 0.01 view 0 90 zoom 1.8
+ dump_modify mydmp backcolor white &
+   acolor OW red acolor HW white &
+   adiam OW 3 adiam HW 1.5
+\end{verbatim}}
+Let us also extract the volume and density in the terminal every 1000 steps:
+{\normalsize \begin{verbatim}
+ variable myvol equal vol
+ variable myoxy equal count(H2O)/3
+ variable myrho equal ${myoxy}/v_myvol
+ thermo 1000
+ thermo_style custom step temp etotal v_myvol v_myrho
 \end{verbatim}}
 The variable \textit{myoxy} corresponds to the number of atoms divided by 3, i.e.
-the number of molecules.
+the number of molecules, and the variable \textit{myrho} is the number of molecules
+divided by the volume of the simulation box, i.e. the density (in $\mathrm{\AA{}}^{-3}$).
 
 Finally, let us set the timestep to 1.0 fs, and run the simulation for 20 ps by
 adding the following lines into \textit{input.lmp}:
 {\normalsize \begin{verbatim}
-timestep 1.0
-run 20000
+ timestep 1.0
+ run 20000
 
-write_data H2O.data
+ write_data H2O.data
 \end{verbatim}}
-The final state is written into \textit{H2O.data}. If you open the \textit{dump.lammpstrj}
-file using VMD, you should see the system quickly reaching its equilibrium volume
-and density (see a snapshot of the equilibrated system in Fig.\,\ref{fig:PEG-water}).
-You can also open the \textit{density.dat} file to ensure that the system converged
-toward the density of liquid water during the 20 ps of simulation (Fig.\,\ref{fig:PEG-density}).
+% S.G. may be a binary restart file could be used here to illustrate the new functionalities of the GUI?
+The final state is written into \textit{H2O.data}. From the value of \textit{myrho},
+it should be clear that the system is quickly reaching its equilibrium
+density (see a snapshot of the equilibrated system in Fig.\,\ref{fig:PEG-water},
+and the evolution of the density in Fig.\,\ref{fig:PEG-density}).
 
 \begin{figure}
 \centering