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\documentclass[11pt]{article} |
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\usepackage{amsmath} |
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\usepackage{amssymb} |
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\usepackage{endfloat} |
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\usepackage{listings} |
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\usepackage{palatino} |
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\usepackage{graphicx} |
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\usepackage[ref]{overcite} |
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\usepackage{setspace} |
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\usepackage{tabularx} |
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\pagestyle{plain} |
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\pagenumbering{arabic} |
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\oddsidemargin 0.0cm \evensidemargin 0.0cm |
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\topmargin -21pt \headsep 10pt |
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\textheight 9.0in \textwidth 6.5in |
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\brokenpenalty=10000 |
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\renewcommand{\baselinestretch}{1.2} |
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\renewcommand\citemid{\ } % no comma in optional reference note |
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\begin{document} |
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These are the bass keywords. |
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\begin{table} |
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\caption{The Global Keywords: Required 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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\begin{tabularx}{\linewidth}% |
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{>{\setlength{\hsize}{1.00\hsize}}X% |
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>{\setlength{\hsize}{0.4\hsize}}X% |
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>{\setlength{\hsize}{1.2\hsize}}X% |
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>{\setlength{\hsize}{1.4\hsize}}X} |
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{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
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{\tt forceField} & string & Sets the force field. & Possible force fields are "DUFF", "LJ", and "EAM". \\ |
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{\tt ensemble} & string & Sets the ensemble. & Possible ensembles are "NVE", "NVT", "NPTi", "NPTf", and "NPTxyz".\\ |
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{\tt dt} & fs & Sets the time step. & Selection of {\tt dt} should be small enough to sample the fastest motion of the simulation. \\ |
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{\tt nComponents} & integer & Sets the number of components. & Needs to appear before the first {\tt Component} block. \\ |
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{\tt initialConfig} & string & Sets the file containing the initial configuration. & Can point to any file containing the configuration in the correct order. |
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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{The Global Keywords: General 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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\begin{tabularx}{\linewidth}% |
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{>{\setlength{\hsize}{1.00\hsize}}X% |
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>{\setlength{\hsize}{0.4\hsize}}X% |
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>{\setlength{\hsize}{1.2\hsize}}X% |
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>{\setlength{\hsize}{1.4\hsize}}X} |
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{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
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{\tt finalConfig} & string & Option to set the name of the final output file. & Useful when stringing simulations together. Defaults to the {\tt .bass} file with an {\tt .eor} extension. \\ |
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{\tt runTime} & fs & Sets the time at which the simulation should end. & The time is an absolute time, and will end the simulation when the current time meets or exceeds the {\tt runTime}. \\ |
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{\tt useInitialTime} & logical & Sets whether the initial time is taken from the {\tt .init} file. & Useful when recovering a simulation from a crashed processor. Default is false. \\ |
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{\tt sampleTime} & fs & Sets the frequency at which the {\tt .dump} file is written. & Default sets the frequency to the {\tt runTime}. \\ |
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{\tt statusTime} & fs & Sets the frequency at which the {\tt .stat} file is written. & Defaults sets the frequency to the {\tt sampleTime}. \\ |
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{\tt LJrcut} & $\mbox{\AA}$ & Manually sets the Lennard-Jones cutoff. & Defaults to $2.5\sigma_L$, where $\sigma_L$ is the largest LJ $\sigma$ in the simulation. \\ |
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{\tt electrostaticCutoffRadius}& & & \\ |
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& $\mbox{\AA}$ & Manually sets the cutoff used by the electrostatic potentials. & Defaults to $15\mbox{\AA}$ \\ |
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{\tt electrostaticSkinThickness} & & & \\ |
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& $\mbox{\AA}$ & Manually sets the skin thickness for the electrostatic switching function. & Defaults to 5~\% of the {\tt electrostaticSkinThickness}. \\ |
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{\tt useReactionField} & logical & Turns the reaction field correction on/off. & Default is "false". \\ |
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{\tt dielectric} & unitless & Sets the dielectric constant for reaction field. & If {\tt useReactionField} is true, then {\tt dielectric} must be set. \\ |
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{\tt usePeriodicBoundaryConditions} & & & \\ |
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& logical & Turns periodic boundary conditions on/off. & Default is "true". \\ |
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{\tt seed } & integer & Sets the seed value for the random number generator. & The seed needs to be at least 9 digits long. The default is to take the seed from the CPU clock. |
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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{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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\begin{tabularx}{\linewidth}% |
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{>{\setlength{\hsize}{1.00\hsize}}X% |
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>{\setlength{\hsize}{0.4\hsize}}X% |
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>{\setlength{\hsize}{1.2\hsize}}X% |
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>{\setlength{\hsize}{1.4\hsize}}X} |
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{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
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{\tt tempSet} & logical & Turns Boltzmann sampling of velocities on/off. & Should only be used in the NVE ensemble. Default is "false". \\ |
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{\tt thermalTime} & fs & Sets the frequency of the velocity resampling when {\tt tempSet} is true. & Default frequency is set to the {\tt runTime} (\emph{i.e.}~once at the beginning only). \\ |
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{\tt targetTemp } & K & Sets the target temperature. & Used when re-scaling the velocities and by the constant temperature ensembles. \\ |
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{\tt targetPressure} & atm & Sets the target pressure. & Used in the constant pressure ensembles. \\ |
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{\tt tauThermostat} & fs & Sets the $\tau_{\text{thermostat}}$. & Used by the constant temperature integration schemes. \\ |
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{\tt tauBarostat} & fs & Sets the $\tau_{\text{barostat}}$. & Used by the constant pressure integration schemes. \\ |
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{\tt resetTime} & fs & Sets the frequency at which the constant pressure and temperature schemes have their drag coefficients set to 0. & If {\tt resetTime} is not present, then the integrators are only zeroed at the beginning of the run.\\ |
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{\tt useInitialExtendedSystemState} & & & \\ |
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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} |
