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shorten min_coords.data name
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files/tutorial1/solution/improved.md.lmp

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@@ -5,7 +5,7 @@ atom_style atomic
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boundary p p p
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# 2) System definition
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pair_style lj/cut 4.0
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read_data minimized_coordinates.data
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read_data min_coords.data
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region cyl_in cylinder z 0 0 10 INF INF side in
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region cyl_out cylinder z 0 0 10 INF INF side out
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group grp_t1 type 1

files/tutorial1/solution/improved.min.lmp

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@@ -23,5 +23,5 @@ thermo_style custom step etotal press
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# 5) Run
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minimize 1.0e-6 1.0e-6 1000 10000
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# 6) Save status
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write_data minimized_coordinates.data
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write_data min_coords.data
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lammps-tutorials.tex

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@@ -660,9 +660,8 @@ \subsubsection{My first input}
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At this point, you can create a snapshot image of the
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current system using the \guicmd{Image Viewer} window, which can be
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accessed by clicking the \guicmd{Create snapshot image} button at the
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bottom of the LAMMPS-GUI. The image viewer
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works by instructing LAMMPS to render an image of the current system using
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accessed by clicking the \guicmd{Create Image} button in the \guicmd{Run} menu.
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The image viewer works by instructing LAMMPS to render an image of the current system using
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its internal rendering library via the \lmpcmd{dump image} command. The
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resulting image is then displayed, and various buttons allow you to adjust
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the view and rendering style. The image of
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is placed \emph{after} the \lmpcmd{minimize} command):
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\begin{lstlisting}
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# 6) Save system
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write_data minimized_coordinates.data
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write_data min_coords.data
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\end{lstlisting}
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A key improvement to the input is the addition of the
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\lmpcmd{write\_data} command. This command writes the state
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of the system to a text file called \flecmd{minimized\_coordinates.data}.
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of the system to a text file called \flecmd{min\_coords.data}.
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This \flecmd{.data} file will be used later
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to restart the simulation from the final state of the energy
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minimization step without having to repeat the system creation and
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minimization.
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Run the \flecmd{improved.min.lmp} file using LAMMPS. At the end of the simulation, a file
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called \flecmd{minimized\_coordinates.data} is created. You can view the contents
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called \flecmd{min\_coords.data} is created. You can view the contents
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of the file with the file view feature of LAMMPS--GUI, e.g.~from the
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\guicmd{File} menu or by right-clicking on the file name in the editor
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and selecting the entry \guicmd{View file `minimized\_coordinates.data'}.
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and selecting the entry \guicmd{View file `min\_coords.data'}.
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The created \flecmd{.data} file contains all the information necessary to
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restart the simulation, such as the number of atoms, the box size, the
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\begin{lstlisting}
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# 2) System definition
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pair_style lj/cut 4.0
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read_data minimized_coordinates.data
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read_data min_coords.data
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\end{lstlisting}
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By visualizing the system (see figure \ref{fig:improved-min}), you may

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