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96 | 96 | \renewcommand{\floatpagefraction}{0.8} % At least 80% of a page must be used by floats |
97 | 97 | \renewcommand{\textfraction}{0.1} % At least 10% of a page must contain text |
98 | 98 |
|
99 | | -\newcommand{\lmpcmd}[1]{\hspace{0pt}\colorbox{listing}{\textcolor{command}{\small{#1}}}\hspace{0pt}} % lammps command |
| 99 | +% AK: I removed the \hspace{0pt} from \lmpcmd{} since otherwise a following comma |
| 100 | +% or full stop may wrap to the next line. |
| 101 | +\newcommand{\lmpcmd}[1]{\colorbox{listing}{\textcolor{command}{\small{#1}}}} % lammps command |
| 102 | +%\newcommand{\lmpcmd}[1]{\hspace{0pt}\colorbox{listing}{\textcolor{command}{\small{#1}}}\hspace{0pt}} % lammps command |
100 | 103 | % \newcommand{\lmpcmd}[1]{\hspace{0pt}\colorbox{listing}{\textcolor{command}{\texttt{#1}}}\hspace{0pt}} % lammps command |
101 | | -\newcommand{\lmpcmdnote}[1]{\hspace{0pt}\colorbox{note_listing}{\textcolor{command}{\small{#1}}}\hspace{0pt}} % lammps command inside note |
| 104 | +\newcommand{\lmpcmdnote}[1]{\colorbox{note_listing}{\textcolor{command}{\small{#1}}}} % lammps command inside note |
| 105 | +% \newcommand{\lmpcmdnote}[1]{\hspace{0pt}\colorbox{note_listing}{\textcolor{command}{\small{#1}}}\hspace{0pt}} % lammps command inside note |
102 | 106 | \newcommand{\flrcmd}[1]{\textcolor{command}{\texttt{#1}}} % folder in monopace |
103 | 107 | \newcommand{\flecmd}[1]{\textcolor{command}{\texttt{#1}}} % files name in monopace |
104 | 108 | \newcommand{\guicmd}[1]{\textcolor{command}{\texttt{«#1»}}} % LAMMPS-GUI commands in French quotation monopace |
@@ -820,18 +824,18 @@ \subsubsection{My first input} |
820 | 824 | thermo_style custom step temp etotal pe ke press |
821 | 825 | \end{lstlisting} |
822 | 826 |
|
823 | | -Since LAMMPS reads inputs from top to bottom, these lines will |
824 | | -be executed \emph{after} the energy minimization. Therefore, |
825 | | -there is no need to re-initialize or re-define the |
826 | | -system. The \lmpcmd{thermo} command is called a second time to |
827 | | -update the output frequency from 10 to 50 as soon as \lmpcmd{PART B} of |
828 | | -the simulation starts. In addition, a new \lmpcmd{thermo\_style} |
829 | | -command is introduced to specify the thermodynamic information LAMMPS should |
830 | | -print during during \lmpcmd{PART B.} This adjustment is made because, during |
831 | | -molecular dynamics, the system exhibits a non-zero temperature $T$ (and |
832 | | -consequently a non-zero kinetic energy $K$, keyword \lmpcmd{ke}), which are useful to monitor. |
833 | | -The \lmpcmd{pe} keyword represents the potential energy of the system, $U$, such that |
834 | | -$U + K = E$. |
| 827 | +Since LAMMPS reads inputs from top to bottom, these lines will be |
| 828 | +executed \emph{after} the energy minimization. Therefore, there is no |
| 829 | +need to re-initialize or re-define the system. The \lmpcmd{thermo} |
| 830 | +command is called a second time to update the output frequency from 10 |
| 831 | +to 50 as soon as \lmpcmd{PART B} of the simulation starts. In addition, |
| 832 | +a new \lmpcmd{thermo\_style} command is introduced to specify the |
| 833 | +thermodynamic information LAMMPS should print during during \lmpcmd{PART |
| 834 | + B}. This adjustment is made because, during molecular dynamics, the |
| 835 | +system exhibits a non-zero temperature $T$ (and consequently a non-zero |
| 836 | +kinetic energy $K$, keyword \lmpcmd{ke}), which are useful to monitor. |
| 837 | +The \lmpcmd{pe} keyword represents the potential energy of the system, |
| 838 | +$U$, such that $U + K = E$. |
835 | 839 |
|
836 | 840 | Then, add a second \lmpcmd{Run} category by including the following |
837 | 841 | lines in \lmpcmd{PART B} of \flecmd{initial.lmp}: |
@@ -937,7 +941,7 @@ \subsubsection{My first input} |
937 | 941 | commands across multiple lines. These two commands tell} LAMMPS to |
938 | 942 | generate NetPBM format images every 100 |
939 | 943 | steps. The two \lmpcmd{type} keywords are for \lmpcmd{color} and |
940 | | -\lmpcmd{diameter,} respectively. Run the \flecmd{initial.lmp} using |
| 944 | +\lmpcmd{diameter}, respectively. Run the \flecmd{initial.lmp} using |
941 | 945 | LAMMPS again, and a new window named \guicmd{Slide Show} will pop up. |
942 | 946 | It will show each image created by the \lmpcmd{dump image} as it is |
943 | 947 | created. After the simulation is finished (or stopped), the slideshow |
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