diff --git a/src/CLToolDriver.cpp b/src/CLToolDriver.cpp index 0f3e1e01be90738a4a155e84d70dbb549881fd1e..ef5eca096b9734ebe72ad7e95f28acc2ccafb60c 100644 --- a/src/CLToolDriver.cpp +++ b/src/CLToolDriver.cpp @@ -44,11 +44,23 @@ The input to driver is specified using the command line arguments described belo \par Examples The following command tells plumed to postprocess the trajectory contained in trajectory.xyz - by calcualting the actions described in the input file plumed.dat. + by performing the actions described in the input file plumed.dat. Actions that take the +stride keyword will be run for every frame in the trajectory. The specific values of the +STRIDE parameters in the input for PRINT,METAD,HISTOGRAM,etc will be ignored. \verbatim plumed driver --plumed plumed.dat --ixyz trajectory.xyz \endverbatim +The following command tells plumed to postprocess the trajectory contained in trajectory.xyz. + by performing the actions described in the input file plumed.dat. Here though +--trajectory-stride is set equal to the frequency with which frames were output during the trajectory +and the --timestep is equal to the simulation timestep. As such the STRIDE parameters in the plumed.dat +files are no longer ignored and any files output resemble those that would have been generated +had we run the calculation we are running with driver when the MD simulation was running. +\verbatim +plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001 +\endverbatim + */ //+ENDPLUMEDOC @@ -66,8 +78,8 @@ void CLToolDriver<real>::registerKeywords( Keywords& keys ){ CLTool::registerKeywords( keys ); keys.addFlag("--help-debug",false,"print special options that can be used to create regtests"); keys.add("compulsory","--plumed","plumed.dat","specify the name of the plumed input file"); - keys.add("compulsory","--timestep","0.001","the timestep for the trajectory in picoseconds"); - keys.add("compulsory","--stride","1","stride between frames on which to do the calculation"); + keys.add("compulsory","--timestep","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds"); + keys.add("compulsory","--stride","1","the frequency with which frames were output to this trajectory during the simulation"); keys.add("atoms","--ixyz","the trajectory in xyz format"); keys.add("optional","--length-units","units for length, either as a string or a number"); keys.add("optional","--dump-forces","dump the forces on a file");