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\begin{table} |
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\caption{The Global Keywords} |
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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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>{\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. & Simulation will fail if not present. \\ |
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{\tt ensemble} & string & Sets the ensemble. & Simulation will fail if not present. \\ |
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{\tt dt} & fs & Sets the time step. & Simulation will fail if not present. \\ |
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{\tt nComponents} & integer & Sets the number of components. & Simulation will fail if not present. \\ |
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{\tt initialConfig} & string & Sets the file containing the initial configuration. & Simulation will fail if not present.\\ |
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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 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} |
