void ActionWithAveraging::registerKeywords( Keywords& keys ) {
Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );
ActionWithArguments::registerKeywords( keys ); ActionWithValue::registerKeywords( keys ); ActionWithVessel::registerKeywords( keys );
keys.add("compulsory","STRIDE","1","the frequency with which the data should be collected and added to the quantity being averaged");
keys.add("compulsory","CLEAR","0","the frequency with which to clear all the accumulated data. The default value "
"of 0 implies that all the data will be used and that the grid will never be cleared");
keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
keys.addFlag("UNORMALIZED",false,"output the unaveraged quantity/quantities."); keys.remove("NUMERICAL_DERIVATIVES");
}
void ActionVolume::registerKeywords( Keywords& keys ){
VolumeGradientBase::registerKeywords( keys );
if( keys.reserved("VMEAN") ) keys.use("VMEAN");
keys.use("MEAN"); keys.use("LESS_THAN"); keys.use("MORE_THAN");
keys.use("BETWEEN"); keys.use("HISTOGRAM");
keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation");
keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used");
keys.addFlag("OUTSIDE",false,"calculate quantities for colvars that are on atoms outside the region of interest");
}
void Mapping::registerKeywords( Keywords& keys ){
Action::registerKeywords( keys );
ActionWithValue::registerKeywords( keys );
ActionWithArguments::registerKeywords( keys );
ActionAtomistic::registerKeywords( keys );
vesselbase::ActionWithVessel::registerKeywords( keys );
keys.add("compulsory","REFERENCE","a pdb file containing the set of reference configurations");
keys.add("compulsory","PROPERTY","the property to be used in the index. This should be in the REMARK of the reference");
keys.add("compulsory","TYPE","OPTIMAL","the manner in which distances are calculated");
keys.addFlag("DISABLE_CHECKS",false,"disable checks on reference input structures.");
}
void FuncSumHills::registerKeywords(Keywords& keys){
Function::registerKeywords(keys);
keys.use("ARG");
keys.add("optional","HILLSFILES"," source file for hills creation(may be the same as HILLS)"); // this can be a vector!
keys.add("optional","HISTOFILES"," source file for histogram creation(may be the same as HILLS)"); // also this can be a vector!
keys.add("optional","HISTOSIGMA"," sigmas for binning when the histogram correction is needed ");
keys.add("optional","PROJ"," only with sumhills: the projection on the cvs");
keys.add("optional","KT"," only with sumhills: the kt factor when projection on cvs");
keys.add("optional","GRID_MIN","the lower bounds for the grid");
keys.add("optional","GRID_MAX","the upper bounds for the grid");
keys.add("optional","GRID_BIN","the number of bins for the grid");
keys.add("optional","OUTHILLS"," output file for hills ");
keys.add("optional","OUTHISTO"," output file for histogram ");
keys.add("optional","INITSTRIDE"," stride if you want an initial dump ");
keys.add("optional","STRIDE"," stride when you do it on the fly ");
keys.addFlag("ISCLTOOL",true,"use via plumed commandline: calculate at read phase and then go");
keys.addFlag("PARALLELREAD",false,"read parallel HILLS file");
keys.addFlag("NEGBIAS",false,"dump negative bias ( -bias ) instead of the free energy: needed in welltempered with flexible hills ");
keys.addFlag("NOHISTORY",false,"to be used with INITSTRIDE: it splits the bias/histogram in pieces without previous history ");
keys.add("optional","FMT","the format that should be used to output real numbers");
}
void Driver<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","1.0","the timestep that was used in the calculation that produced this trajectory in picoseconds");
keys.add("compulsory","--trajectory-stride","1","the frequency with which frames were output to this trajectory during the simulation");
keys.add("compulsory","--multi","0","set number of replicas for multi environment (needs mpi)");
keys.addFlag("--noatoms",false,"don't read in a trajectory. Just use colvar files as specified in plumed.dat");
keys.add("atoms","--ixyz","the trajectory in xyz format");
keys.add("atoms","--igro","the trajectory in gro 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");
keys.add("optional","--dump-forces-fmt","( default=%%f ) the format to use to dump the forces");
keys.add("optional","--pdb","provides a pdb with masses and charges");
keys.add("optional","--box","comma-separated box dimensions (3 for orthorombic, 9 for generic)");
keys.add("hidden","--debug-float","turns on the single precision version (to check float interface)");
keys.add("hidden","--debug-dd","use a fake domain decomposition");
keys.add("hidden","--debug-pd","use a fake particle decomposition");
keys.add("hidden","--debug-grex","use a fake gromacs-like replica exchange, specify exchange stride");
keys.add("hidden","--debug-grex-log","log file for debug=grex");
}
void SecondaryStructureRMSD::registerKeywords( Keywords& keys ) {
Action::registerKeywords( keys );
ActionWithValue::registerKeywords( keys );
ActionAtomistic::registerKeywords( keys );
keys.add("residues","RESIDUES","this command is used to specify the set of residues that could conceivably form part of the secondary structure. "
"It is possible to use residues numbers as the various chains and residues should have been identified else using an instance of the "
"\\ref MOLINFO action. If you wish to use all the residues from all the chains in your system you can do so by "
"specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues "
"you are interested in as a list of numbers. Please be aware that to form secondary structure elements your chain "
"must contain at least N residues, where N is dependent on the particular secondary structure you are interested in. "
"As such if you define portions of the chain with fewer than N residues the code will crash.");
keys.add("compulsory","TYPE","DRMSD","the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. "
"For more details on the OPTIMAL and SIMPLE methods see \\ref RMSD. For more details on the "
"DRMSD method see \\ref DRMSD.");
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions");
keys.add("compulsory","R_0","0.08","The r_0 parameter of the switching function.");
keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
keys.add("compulsory","NN","8","The n parameter of the switching function");
keys.add("compulsory","MM","12","The m parameter of the switching function");
keys.reserve("optional","STRANDS_CUTOFF","If in a segment of protein the two strands are further apart then the calculation "
"of the actual RMSD is skipped as the structure is very far from being beta-sheet like. "
"This keyword speeds up the calculation enormously when you are using the LESS_THAN option. "
"However, if you are using some other option, then this cannot be used");
keys.addFlag("VERBOSE",false,"write a more detailed output");
keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
"that contributed less than TOL at the previous neighbor list update step are ignored.");
ActionWithVessel::registerKeywords( keys );
keys.use("LESS_THAN"); keys.use("MIN"); keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST");
keys.setComponentsIntroduction("By default this Action calculates the number of structural units that are within a certain "
"distance of a idealized secondary structure element. This quantity can then be referenced "
"elsewhere in the input by using the label of the action. However, this Action can also be used to "
"calculate the following quantities by using the keywords as described below. The quantities then "
"calculated can be referenced using the label of the action followed by a dot and then the name "
"from the table below. Please note that you can use the LESS_THAN keyword more than once. The resulting "
"components will be labelled <em>label</em>.lessthan-1, <em>label</em>.lessthan-2 and so on unless you "
"exploit the fact that these labels can be given custom labels by using the LABEL keyword in the "
"description of you LESS_THAN function that you are computing");
}
void MultiColvarBase::registerKeywords( Keywords& keys ){
Action::registerKeywords( keys );
ActionWithValue::registerKeywords( keys );
ActionAtomistic::registerKeywords( keys );
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
ActionWithVessel::registerKeywords( keys );
keys.use("NL_TOL");
keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
"that contributed less than TOL at the previous neighbor list update step are ignored.");
keys.setComponentsIntroduction("When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in "
"regular collective variables. The label is used to reference the full set of quantities calculated by "
"the action. This is usual when using \\ref multicolvarfunction. Generally when doing this the previously calculated "
"multicolvar will be referenced using the DATA keyword rather than ARG.\n\n"
"This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by "
"employing the keywords listed below. "
"These quantities can then be referenced elsewhere in the input file by using this Action's label "
"followed by a dot and the name of the quantity. Some amongst them can be calculated multiple times "
"with different parameters. In this case the quantities calculated can be referenced elsewhere in the "
"input by using the name of the quantity followed by a numerical identifier "
"e.g. <em>label</em>.lessthan-1, <em>label</em>.lessthan-2 etc. When doing this and, for clarity we have "
"made the label of the components customizable. As such by using the LABEL keyword in the description of the keyword "
"input you can customize the component name");
}
void Colvar::registerKeywords( Keywords& keys ){
Action::registerKeywords( keys );
ActionWithValue::registerKeywords( keys );
ActionAtomistic::registerKeywords( keys );
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
}
void CLTool::registerKeywords( Keywords& keys ){
keys.addFlag("--help/-h",false,"print this help");
}
void ActionWithValue::noAnalyticalDerivatives(Keywords& keys) {
keys.remove("NUMERICAL_DERIVATIVES");
keys.addFlag("NUMERICAL_DERIVATIVES",true,"analytical derivatives are not implemented for this keyword so numerical derivatives are always used");
}
void PathBase::registerKeywords( Keywords& keys ){
Mapping::registerKeywords( keys );
keys.add("compulsory","LAMBDA","the value of the lambda parameter for paths");
keys.addFlag("NOZPATH",false,"do not calculate the zpath position");
}
