C++ Keywords::add方法代码示例

void PathMSDBase::registerKeywords(Keywords& keys){
  Colvar::registerKeywords(keys);
  keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
  keys.add("compulsory","REFERENCE","the pdb is needed to provide the various milestones");
  keys.add("optional","NEIGH_SIZE","size of the neighbor list");
  keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
}

void GridPrintingBase::registerKeywords( Keywords& keys ){
  Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys );
  keys.add("compulsory","GRID","the action that creates the grid you would like to output");
  keys.add("compulsory","STRIDE","0","the frequency with which the grid should be output to the file.  The default "
                                     "value of 0 ensures that the grid is only output at the end of the trajectory");
  keys.add("compulsory","FILE","density","the file on which to write the grid.");
  keys.add("optional","FMT","the format that should be used to output real numbers");
}

void ContourFindingBase::registerKeywords( Keywords& keys ){
  ActionWithInputGrid::registerKeywords( keys );
  keys.add("compulsory","CONTOUR","the value we would like to draw the contour at in the space");
  keys.add("compulsory","FILE","file on which to output coordinates");
  keys.add("compulsory","UNITS","PLUMED","the units in which to print out the coordinates. PLUMED means internal PLUMED units");
  keys.add("optional", "PRECISION","The number of digits in trajectory file");
  keys.remove("KERNEL"); keys.remove("BANDWIDTH");
}

void SetupMolInfo::registerKeywords( Keywords& keys ) {
  ActionSetup::registerKeywords(keys);
  keys.add("compulsory","STRUCTURE","a file in pdb format containing a reference structure. "
           "This is used to defines the atoms in the various residues, chains, etc . "
           "For more details on the PDB file format visit http://www.wwpdb.org/docs.html");
  keys.add("compulsory","MOLTYPE","protein","what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible");
  keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.");
}

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.use("SUM");
  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 CoordinationBase::registerKeywords( Keywords& keys ) {
  Colvar::registerKeywords(keys);
  keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
  keys.addFlag("PAIR",false,"Pair only 1st element of the 1st group with 1st element in the second, etc");
  keys.addFlag("NLIST",false,"Use a neighbour list to speed up the calculation");
  keys.add("optional","NL_CUTOFF","The cutoff for the neighbour list");
  keys.add("optional","NL_STRIDE","The frequency with which we are updating the atoms in the neighbour list");
  keys.add("atoms","GROUPA","First list of atoms");
  keys.add("atoms","GROUPB","Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)");
}

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 Steinhardt::registerKeywords( Keywords& keys ){
  VectorMultiColvar::registerKeywords( keys ); 
  keys.add("compulsory","NN","12","The n parameter of the switching function ");
  keys.add("compulsory","MM","24","The m parameter of the switching function ");
  keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
  keys.add("compulsory","R_0","The r_0 parameter of the switching function");
  keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
                               "The following provides information on the \\ref switchingfunction that are available. "
                               "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
  keys.use("SPECIES"); keys.use("SPECIESA"); keys.use("SPECIESB");
  keys.use("MEAN"); keys.use("LESS_THAN"); keys.use("MORE_THAN");
  keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS"); keys.use("MIN");
}

void OrientationSphere::registerKeywords( Keywords& keys ){
  multicolvar::MultiColvarFunction::registerKeywords( keys );
  keys.add("compulsory","NN","6","The n parameter of the switching function ");
  keys.add("compulsory","MM","12","The m parameter of the switching function ");
  keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
  keys.add("compulsory","R_0","The r_0 parameter of the switching function");
  keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
                               "The following provides information on the \\ref switchingfunction that are available. "
                               "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
  // Use actionWithDistributionKeywords
  keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("LESS_THAN"); 
  keys.use("MIN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
  keys.use("LOWEST"); keys.use("HIGHEST");
}

void ActionWithVessel::registerKeywords(Keywords& keys){
  keys.add("optional","TOL","this keyword can be used to speed up your calculation. When accumulating sums in which the individual "
                            "terms are numbers inbetween zero and one it is assumed that terms less than a certain tolerance "
                            "make only a small contribution to the sum.  They can thus be safely ignored as can the the derivatives "
                            "wrt these small quantities.");
  keys.reserve("hidden","NL_TOL","this keyword can be used to speed up your calculation.  It must be used in conjuction with the TOL "
                                   "keyword and the value for NL_TOL must be set less than the value for TOL.  This keyword ensures that "
                                   "quantities, which are much less than TOL and which will thus not added to the sums being accumulated "
                                   "are not calculated at every step. They are only calculated when the neighbor list is updated.");
  keys.add("hidden","MAXDERIVATIVES","The maximum number of derivatives that can be used when storing data.  This controls when "
                                     "we have to start using lowmem");
  keys.addFlag("SERIAL",false,"do the calculation in serial.  Do not parallelize");
  keys.addFlag("LOWMEM",false,"lower the memory requirements");
  keys.add( vesselRegister().getKeywords() );
}

void Action::registerKeywords( Keywords& keys ) {
  plumed_assert( keys.size()==0 );
  keys.add( "hidden", "LABEL", "a label for the action so that its output can be referenced in the input to other actions.  Actions with scalar output are referenced using their label only.  Actions with vector output must have a separate label for every component.  Individual componets are then refered to using label.component" );
  keys.reserve("optional","UPDATE_FROM","Only update this action from this time");
  keys.reserve("optional","UPDATE_UNTIL","Only update this action until this time");
  keys.reserve("optional","RESTART","allows per-action setting of restart (YES/NO/AUTO)");
}

void Bias::registerKeywords( Keywords& keys ){
  Action::registerKeywords(keys);
  ActionPilot::registerKeywords(keys);
  ActionWithValue::registerKeywords(keys);
  ActionWithArguments::registerKeywords(keys);
  keys.add("hidden","STRIDE","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
}

void Bias::registerKeywords( Keywords& keys ) {
  Action::registerKeywords(keys);
  ActionPilot::registerKeywords(keys);
  ActionWithValue::registerKeywords(keys);
  ActionWithArguments::registerKeywords(keys);
  keys.add("hidden","STRIDE","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
  componentsAreNotOptional(keys);
  keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
}

void ManyRestraintsBase::registerKeywords( Keywords& keys ) {
    Action::registerKeywords( keys );
    ActionWithValue::registerKeywords( keys );
    ActionWithVessel::registerKeywords( keys );
    ActionWithInputVessel::registerKeywords( keys );
    ActionPilot::registerKeywords( keys );
    keys.add("hidden","STRIDE","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
    keys.remove("TOL");
    keys.addOutputComponent("bias","default","the instantaneous value of the bias potentials");
}