bulk rename files

Author: akohlmey

lammps-tutorials.tex

@@ -544,7 +544,7 @@ \subsubsection{My first input}
 \paragraph{System definition}
 
 The next step is to create the simulation box and put some atoms into it.
-Modify the \textit{System definition} category of \textit{input.lmp} as follows:
+Modify the \textit{System definition} category of \textit{initial.lmp} as follows:
 {\normalsize
 \begin{verbatim}
  # 2) System definition
@@ -599,7 +599,7 @@ \subsubsection{My first input}
 
 \paragraph{Settings}
 Now we provide the settings for the two types of atoms.  Modify the
-\textit{Settings} category of \textit{input.lmp} as follows:
+\textit{Settings} category of \textit{initial.lmp} as follows:
 {\normalsize
 \begin{verbatim}
  # 3) Settings
@@ -656,7 +656,7 @@ \subsubsection{My first input}
 The system is now fully parameterized and the input ready to compute
 forces.  Let us fill in the two last remaining categories,
 \textit{Visualization}, and \textit{Run}, by adding the following lines
-into \textit{input.lmp}:
+into \textit{initial.lmp}:
 {\normalsize
 \begin{verbatim}
  # 4) Visualization
@@ -755,7 +755,7 @@ \subsubsection{My first input}
 and the system is now ready to perform a molecular dynamics simulation
 using the minimized geometry.  Since we want to start from the result of
 the energy minimization step, we can append commands for the MD simulation
-to the same input script, \textit{input.lmp}. After the
+to the same input script, \textit{initial.lmp}. After the
 \textit{minimize} command, add the following lines:
 {\normalsize
 \begin{verbatim}
@@ -781,7 +781,7 @@ \subsubsection{My first input}
 \textit{pe + ke = etotal}.
 
 Then, let us add a second \textit{Run} category by adding the following
-lines to \textit{PART B} of \textit{input.lmp}:
+lines to \textit{PART B} of \textit{initial.lmp}:
 {\normalsize
 \begin{verbatim}
  # 5) Run
@@ -871,7 +871,7 @@ \subsubsection{My first input}
 by either using the \texttt{Ctrl-D} keyboard shortcut or select
 \textit{Copy dump image command} from the \textit{File} menu.  This text
 can be pasted into the into the \textit{Visualization} section of
-\textit{PART B:} of the \textit{input.lmp} file.
+\textit{PART B:} of the \textit{initial.lmp} file.
 
 This may look like the following:
 {\normalsize
@@ -887,7 +887,7 @@ \subsubsection{My first input}
 }
 This command tells LAMMPS to generate NetPBM format images every 100
 steps. The two \textit{type} keywords are for \textit{color} and
-\textit{diameter}, respectively.  Run the \textit{input.lmp} using
+\textit{diameter}, respectively.  Run the \textit{initial.lmp} using
 LAMMPS again, and a new window named \textit{Slide Show} will pop up.
 It will show each image created by the \textit {dump image} as it is
 created and after the simulation is finished (or stopped), the slide
@@ -912,8 +912,8 @@ \subsubsection{Improving the script}
 \paragraph{Control the initial atom positions}
 Create a new folder next to \textit{my-first-input/} and call it
 \textit{improved-input/}. Then, create a new input file within
-\textit{improved-input/} and call it \textit{input.min.lmp}. Similarly to what
-has been done previously, copy the following lines into \textit{input.min.lmp}:
+\textit{improved-input/} and call it \textit{improved.min.lmp}. Similarly to what
+has been done previously, copy the following lines into \textit{improved.min.lmp}:
 {\normalsize
 \begin{verbatim}
  # 1) Initialization
@@ -942,7 +942,7 @@ \subsubsection{Improving the script}
 }
 The \textit{side in} and \textit{side out} keywords are used to define regions
 that are respectively inside and outside of the cylinder of radius 10. Then,
-copy similar lines as previously into \textit{input.min.lmp}:
+copy similar lines as previously into \textit{improved.min.lmp}:
 {\normalsize
 \begin{verbatim}
  # 3) Settings
@@ -976,7 +976,7 @@ \subsubsection{Improving the script}
 \textit{.data} file will be used later to restart the simulation from
 the final state of the energy minimization step.
 
-Run the \textit{input.min.lmp} script.  At the end of the simulation, a
+Run the \textit{improved.min.lmp} script.  At the end of the simulation, a
 file called \textit{minimized\_coordinates.data} is created.  You can
 view the contents of the file either using \textit{View} entry in the
 \textit{File} menu, by using the keyboard shortcut
@@ -1011,7 +1011,7 @@ \subsubsection{Improving the script}
 
 Let us create a new input file and start a molecular dynamics simulation
 directly from the previously saved configuration. Within
-\textit{improved-input/}, create a new file called \textit{input.md.lmp}
+\textit{improved-input/}, create a new file called \textit{improved.md.lmp}
 and copy the same lines as previously:
 {\normalsize
 \begin{verbatim}
@@ -1024,7 +1024,7 @@ \subsubsection{Improving the script}
 }
 Here, instead of creating a new region and adding atoms to it, we can
 simply import the previously saved configuration by adding the following
-command to \textit{input.md.lmp}:
+command to \textit{improved.md.lmp}:
 {\normalsize
 \begin{verbatim}
  # 2) System definition
@@ -1041,7 +1041,7 @@ \subsubsection{Improving the script}
 during minimization.  To start the simulation from a clean slate, with
 only atoms of type 2 within the cylinder and atoms of type 1 outside the
 cylinder, let us delete the misplaced atoms by adding the following
-commands to \textit{input.md.lmp}:
+commands to \textit{improved.md.lmp}:
 
 {\normalsize
 \begin{verbatim}
@@ -1100,7 +1100,7 @@ \subsubsection{Improving the script}
 coordination number is a measure of the average number of type 2 atoms
 in the vicinity of type 1 atoms, which serves as a good indicator of the
 degree of mixing in a binary mixture.  Add the following lines into
-\textit{input.md.lmp}:
+\textit{improved.md.lmp}:
 {\normalsize
 \begin{verbatim}
  compute coor12 group_type_1 coord/atom &
@@ -1120,7 +1120,7 @@ \subsubsection{Improving the script}
 \label{fig:evolution-population}
 \end{figure}
 
-Add the following lines into \textit{input.md.lmp}. Note the absence of
+Add the following lines into \textit{improved.md.lmp}. Note the absence of
 \textit{Settings} section, because the settings are taken from the
 \textit{.data} file.
 {\normalsize
@@ -1143,7 +1143,7 @@ \subsubsection{Improving the script}
 the simulation.
 
 Finally, let us complete the script by adding the following lines into
-\textit{input.md.lmp}:
+\textit{improved.md.lmp}:
 {\normalsize
 \begin{verbatim}
  # 5) Run
@@ -1186,7 +1186,7 @@ \subsubsection{Improving the script}
 due to the drift, which means the system itself cools down.  In the
 extreme case it can freeze and drift very fast. This phenomenon is sometimes referred to as the ``flying ice cube syndrome'' \cite{wong2016good}.
 
-Run \textit{input.md.lmp} and observe the mixing of the two populations
+Run \textit{improved.md.lmp} and observe the mixing of the two populations
 over time (see also Fig.\,\ref{fig:evolution-population}).  From the
 variables \textit{n1\_in} and \textit{n2\_in}, one can follow the number
 of atoms in each region as a function of time