\cvsubsec{Commands to manage the Colvars module}{sec:cvscript_cmdline_cv}
\begin{mdexampleinput}{}
\texttt{\textbf{cv addenergy <E>}}
\\
\-~~~~\texttt{Add an energy to the MD engine (no effect in VMD)}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{E : float - Amount of energy to add}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv config <conf>}}
\\
\-~~~~\texttt{Read configuration from the given string}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{conf : string - Configuration string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv configfile <conf\_file>}}
\\
\-~~~~\texttt{Read configuration from a file}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{conf\_file : string - Path to configuration file}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv delete}}
\\
\-~~~~\texttt{Delete this Colvars module instance (VMD only)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv featurereport}}
\\
\-~~~~\texttt{Return a summary of Colvars features used so far and their citations}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{report : string - Feature report and citations}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv frame [frame]}}
\\
\-~~~~\texttt{Get or set current frame number (VMD only)}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{frame : integer - Frame number (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{frame : integer - Frame number}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomappliedforces}}
\\
\-~~~~\texttt{Get the list of forces applied by Colvars to atoms}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{forces : array of arrays of floats - Atomic forces}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomappliedforcesmax}}
\\
\-~~~~\texttt{Get the maximum norm of forces applied by Colvars to atoms}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{force : float - Maximum atomic force}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomappliedforcesmaxid}}
\\
\-~~~~\texttt{Get the atom ID with the largest applied force}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{id : int - ID of the atom with the maximum atomic force}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomappliedforcesrms}}
\\
\-~~~~\texttt{Get the root-mean-square norm of forces applied by Colvars to atoms}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{force : float - RMS atomic force}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv resetatomappliedforces}}
\\
\-~~~~\texttt{Reset forces applied by Colvars to atoms}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomids}}
\\
\-~~~~\texttt{Get the list of indices of atoms used in Colvars}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{indices : array of ints - Atom indices}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomcharges}}
\\
\-~~~~\texttt{Get the list of charges of atoms used in Colvars}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{charges : array of floats - Atomic charges}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatommasses}}
\\
\-~~~~\texttt{Get the list of masses of atoms used in Colvars}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{masses : array of floats - Atomic masses}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatompositions}}
\\
\-~~~~\texttt{Get the list of cached positions of atoms used in Colvars}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{positions : array of arrays of floats - Atomic positions}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getatomtotalforces}}
\\
\-~~~~\texttt{Get the list of cached total forces of atoms used in Colvars}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{forces : array of arrays of floats - Atomic total foces}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getconfig}}
\\
\-~~~~\texttt{Get the module's configuration string read so far}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{conf : string - Current configuration string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getenergy}}
\\
\-~~~~\texttt{Get the current Colvars energy}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{E : float - Amount of energy (internal units)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getnumactiveatomgroups}}
\\
\-~~~~\texttt{Get the number of atom groups that currently have positive ref counts}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{count : integer - Total number of atom groups}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getnumactiveatoms}}
\\
\-~~~~\texttt{Get the number of atoms that currently have positive ref counts}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{count : integer - Total number of atoms}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getnumatoms}}
\\
\-~~~~\texttt{Get the number of requested atoms, including those not in use now}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{count : integer - Total number of atoms}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getstepabsolute}}
\\
\-~~~~\texttt{Get the current step number of the simulation (including restarts)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{step : int - Absolute step number}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv getsteprelative}}
\\
\-~~~~\texttt{Get the current step number from the start of this job}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{step : int - Relative step number}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv help [command]}}
\\
\-~~~~\texttt{Get the help string of the Colvars scripting interface}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{command : string - Get the help string of this specific command (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{help : string - Help string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv languageversion}}
\\
\-~~~~\texttt{Get the C++ language version number}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{version : string - C++ language version}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv list [param]}}
\\
\-~~~~\texttt{Return a list of all variables or biases}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{param : string - "colvars" or "biases"; default is "colvars" (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{list : sequence of strings - List of elements}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv listcommands}}
\\
\-~~~~\texttt{Get the list of script functions, prefixed with "cv\_", "colvar\_" or "bias\_"}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{list : sequence of strings - List of commands}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv listindexfiles}}
\\
\-~~~~\texttt{Get a list of the index files loaded in this session}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{list : sequence of strings - List of index file names}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv listinputfiles}}
\\
\-~~~~\texttt{Get a list of all input/configuration files loaded in this session}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{list : sequence of strings - List of file names}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv load <prefix>}}
\\
\-~~~~\texttt{Load data from a state file into all matching colvars and biases}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{prefix : string - Path to existing state file or input prefix}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv loadfromstring <buffer>}}
\\
\-~~~~\texttt{Load state data from a string into all matching colvars and biases}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{buffer : string - String buffer containing the state information}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv molid [molid]}}
\\
\-~~~~\texttt{Get or set the molecule ID on which Colvars is defined (VMD only)}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{molid : integer - New molecule ID; -1 means undefined (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{molid : integer - Current molecule ID}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv printframe}}
\\
\-~~~~\texttt{Return the values that would be written to colvars.traj}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{values : string - The values}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv patchversion}}
\\
\-~~~~\texttt{Get the Colvars patch version number (used for bugfixes only)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{version : string - Colvars version}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv printframelabels}}
\\
\-~~~~\texttt{Return the labels that would be written to colvars.traj}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{Labels : string - The labels}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv reset}}
\\
\-~~~~\texttt{Delete all internal configuration}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv resetindexgroups}}
\\
\-~~~~\texttt{Clear the index groups loaded so far, allowing to replace them}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv save <prefix>}}
\\
\-~~~~\texttt{Change the prefix of all output files and save them}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{prefix : string - Output prefix with trailing ".colvars.state" gets removed)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv savetostring}}
\\
\-~~~~\texttt{Write the Colvars state to a string and return it}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : string - The saved state}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv targettemperature [T]}}
\\
\-~~~~\texttt{Get/set target temperature, overriding internally what the MD engine reports}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{T : float - New target temperature in K (internal use) (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{T : float - Current target temperature in K}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv timestep [dt]}}
\\
\-~~~~\texttt{Get/set integration timestep, overriding internally what the MD engine reports}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{dt : float - New integration timestep in MD engine units (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{dt : float - Current integration timestep in MD engine units}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv units [units]}}
\\
\-~~~~\texttt{Get or set the current Colvars unit system}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{units : string - The new unit system (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{units : string - The current unit system}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv update}}
\\
\-~~~~\texttt{Recalculate colvars and biases}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv version}}
\\
\-~~~~\texttt{Get the Colvars version string}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{version : string - Colvars version}
\end{mdexampleinput}
\cvsubsec{Commands to manage individual collective variables}{sec:cvscript_cmdline_colvar}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name addforce <force>}}
\\
\-~~~~\texttt{Apply the given force onto this colvar (no effects outside run)}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{force : float or array - Applied force; must match colvar dimensionality}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{force : float or array - Applied force; matches colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name communicateforces}}
\\
\-~~~~\texttt{Communicate bias forces from this colvar to atoms}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name cvcflags <flags>}}
\\
\-~~~~\texttt{Enable or disable individual components by setting their active flags}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{flags : integer array - Zero/nonzero value disables/enables the CVC}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name delete}}
\\
\-~~~~\texttt{Delete this colvar, along with all biases that depend on it}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name get <feature>}}
\\
\-~~~~\texttt{Get the value of the given feature for this colvar}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{feature : string - Name of the feature}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : 1/0 - State of the given feature}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getappliedforce}}
\\
\-~~~~\texttt{Return the total of the forces applied to this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{force : float - Applied force; matches the colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name resetbiasforce}}
\\
\-~~~~\texttt{Return the total of the forces applied to this colvar}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getatomgroups}}
\\
\-~~~~\texttt{Return the atom indices used by this colvar as a list of lists}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{groups : array of arrays of ints - Atom indices}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getatomids}}
\\
\-~~~~\texttt{Return the list of atom indices used by this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{indices : array of ints - Atom indices}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getconfig}}
\\
\-~~~~\texttt{Return the configuration string of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{conf : string - Current configuration string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getgradients}}
\\
\-~~~~\texttt{Return the atomic gradients of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{gradients : array of arrays of floats - Atomic gradients}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name gettotalforce}}
\\
\-~~~~\texttt{Return the sum of internal and external forces to this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{force : float - Total force; matches the colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name getvolmapids}}
\\
\-~~~~\texttt{Return the list of volumetric map indices used by this colvar}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name help [command]}}
\\
\-~~~~\texttt{Get a help summary or the help string of one colvar subcommand}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{command : string - Get the help string of this specific command (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{help : string - Help string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name modifycvcs <confs>}}
\\
\-~~~~\texttt{Modify configuration of individual components by passing string arguments}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{confs : sequence of strings - New configurations; empty strings are skipped}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name run\_ave}}
\\
\-~~~~\texttt{Get the current running average of the value of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{value : float or array - Averaged value; matches the colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name set <feature> <value>}}
\\
\-~~~~\texttt{Set the given feature of this colvar to a new value}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{feature : string - Name of the feature}
\\
\-~~~~\texttt{value : string - String representation of the new feature value}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name state}}
\\
\-~~~~\texttt{Print a string representation of the feature state of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : string - The feature state}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name type}}
\\
\-~~~~\texttt{Get the type description of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{type : string - Type description}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name update}}
\\
\-~~~~\texttt{Recompute this colvar and return its up-to-date value}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{value : float or array - Current value; matches the colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name value}}
\\
\-~~~~\texttt{Get the current value of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{value : float or array - Current value; matches the colvar dimensionality}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv colvar name width}}
\\
\-~~~~\texttt{Get the width of this colvar}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{width : float - Value of the width}
\end{mdexampleinput}
\cvsubsec{Commands to manage individual biases}{sec:cvscript_cmdline_bias}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name bin}}
\\
\-~~~~\texttt{Get the current grid bin index (flattened if more than 1d)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{bin : integer - Bin index}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name bincount [index]}}
\\
\-~~~~\texttt{Get the number of samples at the given grid bin (1D ABF only for now)}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{index : integer - Grid index; defaults to current bin (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{samples : integer - Number of samples}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name local\_sample\_count [radius]}}
\\
\-~~~~\texttt{Get the number of samples around the current binsamples : integer - Number of samples}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{radius : integer - Sum over radius bins around current bin (optional)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name binnum}}
\\
\-~~~~\texttt{Get the total number of grid points of this bias (1D ABF only for now)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{Bins : integer - Number of grid points}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name delete}}
\\
\-~~~~\texttt{Delete this bias}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name energy}}
\\
\-~~~~\texttt{Get the current energy of this bias}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{E : float - Energy value}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name get <feature>}}
\\
\-~~~~\texttt{Get the value of the given feature for this bias}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{feature : string - Name of the feature}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : 1/0 - State of the given feature}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name getconfig}}
\\
\-~~~~\texttt{Return the configuration string of this bias}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{conf : string - Current configuration string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name help [command]}}
\\
\-~~~~\texttt{Get a help summary or the help string of one bias subcommand}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{command : string - Get the help string of this specific command (optional)}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{help : string - Help string}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name load <prefix>}}
\\
\-~~~~\texttt{Load data into this bias}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{prefix : string - Read from a file with this name or prefix}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name loadfromstring <buffer>}}
\\
\-~~~~\texttt{Load state data into this bias from a string}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{buffer : string - String buffer containing the state information}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name save <prefix>}}
\\
\-~~~~\texttt{Save data from this bias into a file with the given prefix}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{prefix : string - Prefix for the state file of this bias}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name savetostring}}
\\
\-~~~~\texttt{Save data from this bias into a string and return it}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : string - The bias state}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name set <feature> <value>}}
\\
\-~~~~\texttt{Set the given feature of this bias to a new value}
\\
\-~~~~\texttt{\textbf{Parameters}}
\\
\-~~~~\texttt{feature : string - Name of the feature}
\\
\-~~~~\texttt{value : string - String representation of the new feature value}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name share}}
\\
\-~~~~\texttt{Share bias information with other replicas (multiple-walker scheme)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name state}}
\\
\-~~~~\texttt{Print a string representation of the feature state of this bias}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{state : string - String representation of the bias features}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name type}}
\\
\-~~~~\texttt{Print the type of this bias object}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{type : string - Type of this bias object (e.g. metadynamics)}
\end{mdexampleinput}
\begin{mdexampleinput}{}
\texttt{\textbf{cv bias name update}}
\\
\-~~~~\texttt{Recompute this bias and return its up-to-date energy}
\\
\-~~~~\texttt{\textbf{Returns}}
\\
\-~~~~\texttt{E : float - Energy value}
\end{mdexampleinput}
