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\begin{table} |
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\caption{The Global Keywords: Ensemble Parameters} |
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\caption{The Global Keywords: Ensemble/Integrator Parameters} |
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\begin{center} |
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% Note when adding or removing columns, the \hsize numbers must add up to the total number |
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% of columns. |
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& logical & Sets whether the initial state of the constant pressure and temperature integrators is pulled from the {\tt .init} file. & Useful when recovering a simulation from a crashed process. Default is "false". \\ |
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{\tt orthoBoxTolerance} & unitless & Sets the tolerance for orthorhombic/non-orthorhombic box wrapping. & Used mainly in the "NPTf" ensemble. Default is $1\times 10^{-6}$. \\ |
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\end{tabularx} |
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\end{center} |
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\end{table} |
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\begin{table} |
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\caption{{\sc bass} Block Statements} |
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\begin{center} |
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% Note when adding or removing columns, the \hsize numbers must add up to the total number |
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% of columns. |
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\begin{tabularx}{\linewidth}% |
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{>{\setlength{\hsize}{0.5\hsize}}X% |
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>{\setlength{\hsize}{1.2\hsize}}X% |
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>{\setlength{\hsize}{1.3\hsize}}X} |
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{\bf keyword} & {\bf use} & {\bf remarks} \\ \hline |
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{\tt molecule\{\}} & Declares the prototypes of the components. & Can only be declared in the global namespace. \\ |
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{\tt atom\{\}} & Declares the atoms within a molecule or rigid body. & Can only be declared in a molecule or rigid body block. \\ |
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{\tt bond\{\}} & Declares the bonds within a molecule or rigid body. & Can only be declared in a molecule or rigid body block. \\ |
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{\tt bend\{\}} & Declares the bends in a molecule. & Can only be declared in a molecule block. \\ |
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{\tt torsion\{\}} & Declares the torsions in a molecule. & Can only be declared in a molecule block. \\ |
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{\tt component\{\}} & Declares the components present in a simulation. & Can only be declared in the global namespace. \\ |
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\end{tabularx} |
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\end{center} |
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\end{table} |
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\begin{table} |
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\caption{{\sc bass} Pre-Processing Statements} |
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\begin{center} |
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% Note when adding or removing columns, the \hsize numbers must add up to the total number |
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% of columns. |
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\begin{tabularx}{\linewidth}% |
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{>{\setlength{\hsize}{0.8\hsize}}X% |
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>{\setlength{\hsize}{1.0\hsize}}X% |
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>{\setlength{\hsize}{1.2\hsize}}X} |
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{\bf keyword} & {\bf use} & {\bf remarks} \\ \hline |
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{\tt \#include "\emph{file}"} & Includes an external file for processing. & Mainly used to include {\tt .mdl} files into a {\tt .bass} script. \\ |
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{\tt \#define \emph{VARIABLE}} & Declares a pre-processing macro. & Will replace every occurrence of {\tt \emph{VARIABLE}} with whatever follows the define statement. The scope of the define is only to the end of the line, but can span multiple lines using the '$\backslash$'. \\ |
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{\tt \#ifdef \emph{VARIABLE}} & If {\tt \emph{VARIABLE}}is defined, the statements following the {\tt \#ifdef} will be processed. & Closed by an {\tt \#else} or an {\tt \#endif}. Can be nested within another {\tt \#if} directive. \\ |
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{\tt \#ifndef \emph{VARIABLE}} & If {\tt \emph{VARIABLE}} is \emph{not} defined, the statements following the {\tt \#ifndef} will be processed. & Closed by an {\tt \#else} or an {\tt \#endif}. Can be nested within another {\tt \#if } directive. \\ |
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{\tt \#else} & If the preceding {\tt \#if} statement was false, then the statements following the {\tt \#else} will be processed instead. & Closed by the {\tt \#endif} statement. \\ |
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{\tt \#endif} & Ends an {\tt \#if} clause. & All {\tt \#if} clauses must be closed, or the {\sc bass} parser will fail with an error. \\ |
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\end{tabularx} |
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\end{center} |
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\end{table} |
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\end{document} |
