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 ActionWithGrid::registerKeywords( Keywords& keys ){
vesselbase::ActionWithAveraging::registerKeywords( keys );
keys.add("compulsory","BANDWIDTH","the bandwidths for kernel density esimtation");
keys.add("compulsory","KERNEL","gaussian","the kernel function you are using. More details on the kernels available "
"in plumed plumed can be found in \\ref kernelfunctions.");
keys.add("optional","CONCENTRATION","the concentration parameter for Von Mises-Fisher distributions");
}
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");
}
void SwitchingFunction::registerKeywords( Keywords& keys ){
keys.add("compulsory","R_0","the value of R_0 in the switching function");
keys.add("compulsory","D_0","0.0","the value of D_0 in the switching function");
keys.add("optional","D_MAX","the value at which the switching function can be assumed equal to zero");
keys.add("compulsory","NN","6","the value of n in the switching function (only needed for TYPE=RATIONAL)");
keys.add("compulsory","MM","12","the value of m in the switching function (only needed for TYPE=RATIONAL)");
keys.add("compulsory","A","the value of a in the switching funciton (only needed for TYPE=SMAP)");
keys.add("compulsory","B","the value of b in the switching funciton (only needed for TYPE=SMAP)");
}
void MatrixSummationBase::registerKeywords( Keywords& keys ) {
multicolvar::MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","MATRIX","the action that calcualtes the adjacency matrix vessel we would like to analyse");
keys.use("ALT_MIN");
keys.use("LOWEST");
keys.use("HIGHEST");
keys.use("MEAN");
keys.use("MEAN");
keys.use("MIN");
keys.use("MAX");
keys.use("LESS_THAN");
keys.use("MORE_THAN");
keys.use("BETWEEN");
keys.use("HISTOGRAM");
keys.use("MOMENTS");
}
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 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 ActionWithInputMatrix::registerKeywords( Keywords& keys ) {
MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","MATRIX","the action that calcualtes the adjacency matrix vessel we would like to analyse");
}
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");
}
void ActionWithInputVessel::registerKeywords(Keywords& keys) {
keys.add("compulsory","DATA","certain actions in plumed work by calculating a list of variables and summing over them. "
"This particular action can be used to calculate functions of these base variables or prints "
"them to a file. This keyword thus takes the label of one of those such variables as input.");
keys.reserve("compulsory","GRID","the action that creates the input grid you would like to use");
}
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 HistogramBead::registerKeywords( Keywords& keys ) {
keys.add("compulsory","LOWER","the lower boundary for this particular bin");
keys.add("compulsory","UPPER","the upper boundary for this particular bin");
keys.add("compulsory","SMEAR","0.5","the ammount to smear the Gaussian for each value in the distribution");
}
void BridgedMultiColvarFunction::registerKeywords( Keywords& keys ){
MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","DATA","The multicolvar that calculates the set of base quantities that we are interested in");
}
void AnalysisWithLandmarks::registerKeywords( Keywords& keys ) {
Analysis::registerKeywords( keys );
keys.add("compulsory","LANDMARKS","ALL","only use a subset of the data that was collected. "
"For more information on the landmark selection algorithms that are available in "
"plumed see \\ref landmarkselection.");
}
void ClusterAnalysisBase::registerKeywords( Keywords& keys ){
MultiColvarBase::registerKeywords( keys );
keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
}
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 ValueVessel::registerKeywords( Keywords& keys ){
Vessel::registerKeywords( keys );
keys.add("compulsory","COMPONENT","1","the component of the vector for which to calculate this quantity");
}
