| 19 |
|
|
| 20 |
|
\begin{document} |
| 21 |
|
|
| 22 |
+ |
These are the bass keywords. |
| 23 |
+ |
|
| 24 |
+ |
|
| 25 |
|
\begin{table} |
| 26 |
< |
\caption{The Global Keywords} |
| 26 |
> |
\caption{The Global Keywords: Required Parameters} |
| 27 |
|
\begin{center} |
| 28 |
+ |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 29 |
+ |
% of columns. |
| 30 |
|
\begin{tabularx}{\linewidth}% |
| 31 |
< |
{|X| % |
| 32 |
< |
X|% |
| 33 |
< |
X|% |
| 34 |
< |
X|% |
| 30 |
< |
X|} |
| 31 |
> |
{>{\setlength{\hsize}{1.00\hsize}}X% |
| 32 |
> |
>{\setlength{\hsize}{0.4\hsize}}X% |
| 33 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 34 |
> |
>{\setlength{\hsize}{1.4\hsize}}X} |
| 35 |
|
|
| 36 |
< |
{\bf variable}& {\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ |
| 37 |
< |
$\delta t$ & {\tt dt} & fs & Sets the simulation time step. & Simulation will fail if not present. |
| 36 |
> |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 37 |
> |
|
| 38 |
> |
{\tt forceField} & string & Sets the force field. & Possible force fields are "DUFF", "LJ", and "EAM". \\ |
| 39 |
> |
{\tt ensemble} & string & Sets the ensemble. & Possible ensembles are "NVE", "NVT", "NPTi", "NPTf", and "NPTxyz".\\ |
| 40 |
> |
{\tt dt} & fs & Sets the time step. & Selection of {\tt dt} should be small enough to sample the fastest motion of the simulation. \\ |
| 41 |
> |
{\tt nComponents} & integer & Sets the number of components. & Needs to appear before the first {\tt Component} block. \\ |
| 42 |
> |
{\tt initialConfig} & string & Sets the file containing the initial configuration. & Can point to any file containing the configuration in the correct order. \\ |
| 43 |
> |
{\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}. \\ |
| 44 |
> |
|
| 45 |
|
\end{tabularx} |
| 46 |
|
\end{center} |
| 47 |
< |
\end{table} |
| 47 |
> |
\end{table} |
| 48 |
> |
|
| 49 |
> |
|
| 50 |
> |
\begin{table} |
| 51 |
> |
\caption{The Global Keywords: General Parameters} |
| 52 |
> |
\begin{center} |
| 53 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 54 |
> |
% of columns. |
| 55 |
> |
\begin{tabularx}{\linewidth}% |
| 56 |
> |
{>{\setlength{\hsize}{1.00\hsize}}X% |
| 57 |
> |
>{\setlength{\hsize}{0.4\hsize}}X% |
| 58 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 59 |
> |
>{\setlength{\hsize}{1.4\hsize}}X} |
| 60 |
> |
|
| 61 |
> |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 62 |
> |
|
| 63 |
> |
{\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. \\ |
| 64 |
> |
{\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. \\ |
| 65 |
> |
{\tt sampleTime} & fs & Sets the frequency at which the {\tt .dump} file is written. & Default sets the frequency to the {\tt runTime}. \\ |
| 66 |
> |
{\tt statusTime} & fs & Sets the frequency at which the {\tt .stat} file is written. & Defaults sets the frequency to the {\tt sampleTime}. \\ |
| 67 |
> |
{\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. \\ |
| 68 |
> |
{\tt electrostaticCutoffRadius}& & & \\ |
| 69 |
> |
& $\mbox{\AA}$ & Manually sets the cutoff used by the electrostatic potentials. & Defaults to $15\mbox{\AA}$ \\ |
| 70 |
> |
{\tt electrostaticSkinThickness} & & & \\ |
| 71 |
> |
& $\mbox{\AA}$ & Manually sets the skin thickness for the electrostatic switching function. & Defaults to 5~\% of the {\tt electrostaticSkinThickness}. \\ |
| 72 |
> |
{\tt useReactionField} & logical & Turns the reaction field correction on/off. & Default is "false". \\ |
| 73 |
> |
{\tt dielectric} & unitless & Sets the dielectric constant for reaction field. & If {\tt useReactionField} is true, then {\tt dielectric} must be set. \\ |
| 74 |
> |
{\tt usePeriodicBoundaryConditions} & & & \\ |
| 75 |
> |
& logical & Turns periodic boundary conditions on/off. & Default is "true". \\ |
| 76 |
> |
{\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. |
| 77 |
> |
|
| 78 |
> |
\end{tabularx} |
| 79 |
> |
\end{center} |
| 80 |
> |
\end{table} |
| 81 |
> |
|
| 82 |
> |
|
| 83 |
> |
|
| 84 |
> |
\begin{table} |
| 85 |
> |
\caption{The Global Keywords: Ensemble/Integrator Parameters} |
| 86 |
> |
\begin{center} |
| 87 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 88 |
> |
% of columns. |
| 89 |
> |
\begin{tabularx}{\linewidth}% |
| 90 |
> |
{>{\setlength{\hsize}{1.00\hsize}}X% |
| 91 |
> |
>{\setlength{\hsize}{0.4\hsize}}X% |
| 92 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 93 |
> |
>{\setlength{\hsize}{1.4\hsize}}X} |
| 94 |
> |
|
| 95 |
> |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 96 |
> |
|
| 97 |
> |
{\tt tempSet} & logical & Turns Boltzmann sampling of velocities on/off. & Should only be used in the NVE ensemble. Default is "false". \\ |
| 98 |
> |
{\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). \\ |
| 99 |
> |
{\tt targetTemp } & K & Sets the target temperature. & Used when re-scaling the velocities and by the constant temperature ensembles. \\ |
| 100 |
> |
{\tt targetPressure} & atm & Sets the target pressure. & Used in the constant pressure ensembles. \\ |
| 101 |
> |
{\tt tauThermostat} & fs & Sets the $\tau_{\text{thermostat}}$. & Used by the constant temperature integration schemes. \\ |
| 102 |
> |
{\tt tauBarostat} & fs & Sets the $\tau_{\text{barostat}}$. & Used by the constant pressure integration schemes. \\ |
| 103 |
> |
{\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.\\ |
| 104 |
> |
{\tt useInitialExtendedSystemState} & & & \\ |
| 105 |
> |
& 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". \\ |
| 106 |
> |
{\tt orthoBoxTolerance} & unitless & Sets the tolerance for orthorhombic/non-orthorhombic box wrapping. & Used mainly in the "NPTf" ensemble. Default is $1\times 10^{-6}$. \\ |
| 107 |
> |
|
| 108 |
> |
\end{tabularx} |
| 109 |
> |
\end{center} |
| 110 |
> |
\end{table} |
| 111 |
> |
|
| 112 |
> |
\begin{table} |
| 113 |
> |
\caption{The Global Keywords: Energy Minimizer Parameters} |
| 114 |
> |
\begin{center} |
| 115 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 116 |
> |
% of columns. |
| 117 |
> |
\begin{tabularx}{\linewidth}% |
| 118 |
> |
{>{\setlength{\hsize}{1.00\hsize}}X% |
| 119 |
> |
>{\setlength{\hsize}{0.4\hsize}}X% |
| 120 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 121 |
> |
>{\setlength{\hsize}{1.4\hsize}}X} |
| 122 |
> |
|
| 123 |
> |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 124 |
> |
|
| 125 |
> |
{\tt minimizer} & & & \\ |
| 126 |
> |
{\tt minMaxIter} & & & \\ |
| 127 |
> |
{\tt minWriteFreq} & & & \\ |
| 128 |
> |
{\tt minStepSize} & & & \\ |
| 129 |
> |
{\tt minFTol} & & & \\ |
| 130 |
> |
{\tt minGTol} & & & \\ |
| 131 |
> |
{\tt minLSTol} & & & \\ |
| 132 |
> |
{\tt minLSMaxIter} & & & \\ |
| 133 |
> |
|
| 134 |
> |
\end{tabularx} |
| 135 |
> |
\end{center} |
| 136 |
> |
\end{table} |
| 137 |
> |
|
| 138 |
> |
\begin{table} |
| 139 |
> |
\caption{The Global Keywords: Z-Constraint Parameters} |
| 140 |
> |
\begin{center} |
| 141 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 142 |
> |
% of columns. |
| 143 |
> |
\begin{tabularx}{\linewidth}% |
| 144 |
> |
{>{\setlength{\hsize}{1.00\hsize}}X% |
| 145 |
> |
>{\setlength{\hsize}{0.4\hsize}}X% |
| 146 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 147 |
> |
>{\setlength{\hsize}{1.4\hsize}}X} |
| 148 |
> |
|
| 149 |
> |
{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks} \\ \hline |
| 150 |
> |
|
| 151 |
> |
{\tt zconsTime} & & & \\ |
| 152 |
> |
{\tt nZconstraints} & & & \\ |
| 153 |
> |
{\tt zconsForcePolicy} & & & \\ |
| 154 |
> |
{\tt zconsGap} & & & \\ |
| 155 |
> |
{\tt zconsFixtime} & & & \\ |
| 156 |
> |
{\tt zconsUsingSMD} & & & \\ |
| 157 |
> |
|
| 158 |
> |
\end{tabularx} |
| 159 |
> |
\end{center} |
| 160 |
> |
\end{table} |
| 161 |
> |
|
| 162 |
> |
|
| 163 |
> |
\begin{table} |
| 164 |
> |
\caption{{\sc bass} Block Statements} |
| 165 |
> |
\begin{center} |
| 166 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 167 |
> |
% of columns. |
| 168 |
> |
\begin{tabularx}{\linewidth}% |
| 169 |
> |
{>{\setlength{\hsize}{0.5\hsize}}X% |
| 170 |
> |
>{\setlength{\hsize}{1.2\hsize}}X% |
| 171 |
> |
>{\setlength{\hsize}{1.3\hsize}}X} |
| 172 |
> |
|
| 173 |
> |
{\bf keyword} & {\bf use} & {\bf remarks} \\ \hline |
| 174 |
> |
|
| 175 |
> |
{\tt molecule\{\}} & Declares the prototypes of the components. & Can only be declared in the global namespace. \\ |
| 176 |
> |
{\tt atom\{\}} & Declares the atoms within a molecule or rigid body. & Can only be declared in a molecule or rigid body block. \\ |
| 177 |
> |
{\tt bond\{\}} & Declares the bonds within a molecule or rigid body. & Can only be declared in a molecule or rigid body block. \\ |
| 178 |
> |
{\tt bend\{\}} & Declares the bends in a molecule. & Can only be declared in a molecule block. \\ |
| 179 |
> |
{\tt torsion\{\}} & Declares the torsions in a molecule. & Can only be declared in a molecule block. \\ |
| 180 |
> |
{\tt component\{\}} & Declares the components present in a simulation. & Can only be declared in the global namespace. \\ |
| 181 |
> |
|
| 182 |
> |
\end{tabularx} |
| 183 |
> |
\end{center} |
| 184 |
> |
\end{table} |
| 185 |
> |
|
| 186 |
> |
\begin{table} |
| 187 |
> |
\caption{{\sc bass} Pre-Processing Statements} |
| 188 |
> |
\begin{center} |
| 189 |
> |
% Note when adding or removing columns, the \hsize numbers must add up to the total number |
| 190 |
> |
% of columns. |
| 191 |
> |
\begin{tabularx}{\linewidth}% |
| 192 |
> |
{>{\setlength{\hsize}{0.8\hsize}}X% |
| 193 |
> |
>{\setlength{\hsize}{1.0\hsize}}X% |
| 194 |
> |
>{\setlength{\hsize}{1.2\hsize}}X} |
| 195 |
> |
|
| 196 |
> |
{\bf keyword} & {\bf use} & {\bf remarks} \\ \hline |
| 197 |
> |
|
| 198 |
> |
{\tt \#include "\emph{file}"} & Includes an external file for processing. & Mainly used to include {\tt .mdl} files into a {\tt .bass} script. \\ |
| 199 |
> |
{\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 '$\backslash$'. \\ |
| 200 |
> |
{\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. \\ |
| 201 |
> |
{\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. \\ |
| 202 |
> |
{\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. \\ |
| 203 |
> |
{\tt \#endif} & Ends an {\tt \#if} clause. & All {\tt \#if} clauses must be closed, or the {\sc bass} parser will fail with an error. \\ |
| 204 |
> |
|
| 205 |
> |
\end{tabularx} |
| 206 |
> |
\end{center} |
| 207 |
> |
\end{table} |
| 208 |
> |
|
| 209 |
> |
\end{document} |
