Added value types to documentation for components

regtest/basic/rt-make-load/Distance10.cpp

@@ -46,6 +46,7 @@ void Distance::registerKeywords( Keywords& keys ){
   Colvar::registerKeywords( keys );
   keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the DISTANCE between this pair of atoms");
 }
 
 Distance::Distance(const ActionOptions&ao):

regtest/basic/rt-make-load/Distance20.cpp

@@ -46,6 +46,7 @@ void Distance::registerKeywords( Keywords& keys ){
   Colvar::registerKeywords( keys );
   keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the DISTANCE between this pair of atoms");
 }
 
 Distance::Distance(const ActionOptions&ao):

regtest/basic/rt15-mklib/Distance2.cpp

@@ -36,6 +36,7 @@ void Distance::registerKeywords( Keywords& keys ){
   Colvar::registerKeywords( keys );
   keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the distance between the input atoms");
 }
 
 Distance::Distance(const ActionOptions&ao):

regtest/basic/rt15/Distance2.cpp

@@ -46,6 +46,7 @@ void Distance::registerKeywords( Keywords& keys ){
   Colvar::registerKeywords( keys );
   keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the distance between the input atoms");
 }
 
 Distance::Distance(const ActionOptions&ao):

regtest/basic/rt15/Distance3.cpp

@@ -46,6 +46,7 @@ void Distance::registerKeywords( Keywords& keys ){
   Colvar::registerKeywords( keys );
   keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the distance between the input atoms");
 }
 
 Distance::Distance(const ActionOptions&ao):

regtest/contour/rt-parse-only/values.json.reference

@@ -76,12 +76,6 @@
 "dens_dist.y" : { "type": "vector", "desciption": "" }
 "dens_dist.z" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dens_dist" : { 
-"action" : "DISTANCES", 
-"dens_dist.x" : { "type": "vector", "desciption": "" }
-"dens_dist.y" : { "type": "vector", "desciption": "" }
-"dens_dist.z" : { "type": "vector", "desciption": "" }
-}, 
 "dens_numer_sigma" : { 
 "action" : "CONSTANT", 
 "dens_numer_sigma" : { "type": "vector", "desciption": "" }

src/adjmat/AdjacencyMatrixBase.cpp

@@ -38,11 +38,11 @@ void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) {
   keys.addFlag("NOPBC",false,"don't use pbc");
   keys.add("compulsory","NL_CUTOFF","0.0","The cutoff for the neighbor list.  A value of 0 means we are not using a neighbor list");
   keys.add("compulsory","NL_STRIDE","1","The frequency with which we are updating the atoms in the neighbor list");
-  keys.addOutputComponent("w","COMPONENTS","a matrix containing the weights for the bonds between each pair of atoms");
-  keys.addOutputComponent("x","COMPONENTS","the projection of the bond on the x axis");
-  keys.addOutputComponent("y","COMPONENTS","the projection of the bond on the y axis");
-  keys.addOutputComponent("z","COMPONENTS","the projection of the bond on the z axis");
-  keys.setValueDescription("a matrix containing the weights for the bonds between each pair of atoms");
+  keys.addOutputComponent("w","COMPONENTS","matrix","a matrix containing the weights for the bonds between each pair of atoms");
+  keys.addOutputComponent("x","COMPONENTS","matrix","the projection of the bond on the x axis");
+  keys.addOutputComponent("y","COMPONENTS","matrix","the projection of the bond on the y axis");
+  keys.addOutputComponent("z","COMPONENTS","matrix","the projection of the bond on the z axis");
+  keys.setValueDescription("matrix","a matrix containing the weights for the bonds between each pair of atoms");
 }
 
 AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):

src/adjmat/Bridge.cpp

@@ -55,7 +55,7 @@ void Bridge::registerKeywords(Keywords& keys) {
   keys.add("optional","SWITCHB","The switchingfunction on the distance between the bridging atoms and the atoms in "
            "group B");
   keys.needsAction("BRIDGE_MATRIX"); keys.needsAction("SUM");
-  keys.setValueDescription("the number of bridging atoms between the two groups");
+  keys.setValueDescription("scalar","the number of bridging atoms between the two groups");
 }
 
 Bridge::Bridge(const ActionOptions& ao):

src/adjmat/Neighbors.cpp

@@ -55,7 +55,7 @@ void Neighbors::registerKeywords( Keywords& keys ) {
   ActionWithMatrix::registerKeywords( keys ); keys.use("ARG");
   keys.add("compulsory","NLOWEST","0","in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one");
   keys.add("compulsory","NHIGHEST","0","in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one");
-  keys.setValueDescription("a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise");
+  keys.setValueDescription("matrix","a matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise");
 }
 
 Neighbors::Neighbors(const ActionOptions&ao):

src/adjmat/TorsionsMatrix.cpp

@@ -55,7 +55,7 @@ void TorsionsMatrix::registerKeywords( Keywords& keys ) {
   ActionWithMatrix::registerKeywords(keys); keys.use("ARG");
   keys.add("atoms","POSITIONS1","the positions to use for the molecules specified using the first argument");
   keys.add("atoms","POSITIONS2","the positions to use for the molecules specified using the second argument");
-  keys.setValueDescription("the matrix of torsions between the two vectors of input directors");
+  keys.setValueDescription("matrix","the matrix of torsions between the two vectors of input directors");
 }
 
 TorsionsMatrix::TorsionsMatrix(const ActionOptions&ao):

src/annfunc/ANN.cpp

@@ -121,7 +121,7 @@ void ANN::registerKeywords( Keywords& keys ) {
   keys.add("numbered", "BIASES", "bias array for each layer of the neural network, "
            "BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, ...");
   // since v2.2 plumed requires all components be registered
-  keys.addOutputComponent("node", "default", "components of ANN outputs");
+  keys.addOutputComponent("node", "default", "scalar", "components of ANN outputs");
 }
 
 ANN::ANN(const ActionOptions&ao):

src/bias/ABMD.cpp

@@ -102,8 +102,8 @@ void ABMD::registerKeywords(Keywords& keys) {
   keys.add("optional","MIN","Array of starting values for the bias (set rho_m(t), otherwise it is set using the current value of ARG)");
   keys.add("optional","NOISE","Array of white noise intensities (add a temperature to the ABMD)");
   keys.add("optional","SEED","Array of seeds for the white noise (add a temperature to the ABMD)");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
-  keys.addOutputComponent("_min","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("_min","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           " These quantities will be named with the arguments of the bias followed by "
                           "the character string _min. These quantities tell the user the minimum value assumed by rho_m(t).");
 }

src/bias/Bias.cpp

@@ -53,7 +53,7 @@ void Bias::registerKeywords( Keywords& 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");
-  keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
+  keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
 }
 
 void Bias::apply() {

src/bias/BiasValue.cpp

@@ -85,7 +85,7 @@ void BiasValue::registerKeywords(Keywords& keys) {
   Bias::registerKeywords(keys);
   keys.use("ARG");
   // Should be _bias below
-  keys.addOutputComponent("_bias","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("_bias","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "these quantities will named with  the arguments of the bias followed by "
                           "the character string _bias. These quantities tell the user how much the bias is "
                           "due to each of the colvars.");

src/bias/ExtendedLagrangian.cpp

@@ -134,10 +134,10 @@ void ExtendedLagrangian::registerKeywords(Keywords& keys) {
   keys.add("compulsory","TAU","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
   keys.add("compulsory","FRICTION","0.0","add a friction to the variable");
   keys.add("optional","TEMP","the system temperature - needed when FRICTION is present. If not provided will be taken from MD code (if available)");
-  keys.addOutputComponent("_fict","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("_fict","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "These quantities will named with the arguments of the bias followed by "
                           "the character string _tilde. It is possible to add forces on these variable.");
-  keys.addOutputComponent("_vfict","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("_vfict","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "These quantities will named with the arguments of the bias followed by "
                           "the character string _tilde. It is NOT possible to add forces on these variable.");
 }

src/bias/LWalls.cpp

@@ -93,7 +93,7 @@ void LWalls::registerKeywords(Keywords& keys) {
   keys.add("compulsory","OFFSET","0.0","the offset for the start of the wall.  The o_i in the expression for a wall.");
   keys.add("compulsory","EXP","2.0","the powers for the walls.  The e_i in the expression for a wall.");
   keys.add("compulsory","EPS","1.0","the values for s_i in the expression for a wall");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
 }
 
 LWalls::LWalls(const ActionOptions&ao):

src/bias/MaxEnt.cpp

@@ -187,13 +187,13 @@ void MaxEnt::registerKeywords(Keywords& keys) {
   keys.addFlag("REWEIGHT",false,"to be used with plumed driver in order to reweight a trajectory a posteriori");
   keys.addFlag("NO_BROADCAST",false,"If active will avoid Lagrangian multipliers to be communicated to other replicas.");
   keys.add("optional","TEMP","the system temperature.  This is required if you are reweighting.");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
-  keys.addOutputComponent("work","default","the instantaneous value of the work done by the biasing force");
-  keys.addOutputComponent("_work","default","the instantaneous value of the work done by the biasing force for each argument. "
+  keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("work","default","scalar","the instantaneous value of the work done by the biasing force");
+  keys.addOutputComponent("_work","default","scalar","the instantaneous value of the work done by the biasing force for each argument. "
                           "These quantities will named with the arguments of the bias followed by "
                           "the character string _work.");
-  keys.addOutputComponent("_error","default","Instantaneous values of the discrepancy between the observable and the restraint center");
-  keys.addOutputComponent("_coupling","default","Instantaneous values of Lagrangian multipliers. They are also written by default in a separate output file.");
+  keys.addOutputComponent("_error","default","scalar","Instantaneous values of the discrepancy between the observable and the restraint center");
+  keys.addOutputComponent("_coupling","default","scalar","Instantaneous values of Lagrangian multipliers. They are also written by default in a separate output file.");
   keys.use("RESTART");
 }
 MaxEnt::MaxEnt(const ActionOptions&ao):

src/bias/MetaD.cpp

@@ -520,16 +520,16 @@ PLUMED_REGISTER_ACTION(MetaD,"METAD")
 
 void MetaD::registerKeywords(Keywords& keys) {
   Bias::registerKeywords(keys);
-  keys.addOutputComponent("rbias","CALC_RCT","the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]."
+  keys.addOutputComponent("rbias","CALC_RCT","scalar","the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]."
                           "This component can be used to obtain a reweighted histogram.");
-  keys.addOutputComponent("rct","CALC_RCT","the reweighting factor c(t).");
-  keys.addOutputComponent("work","CALC_WORK","accumulator for work");
-  keys.addOutputComponent("acc","ACCELERATION","the metadynamics acceleration factor");
-  keys.addOutputComponent("maxbias", "CALC_MAX_BIAS", "the maximum of the metadynamics V(s, t)");
-  keys.addOutputComponent("transbias", "CALC_TRANSITION_BIAS", "the metadynamics transition bias V*(t)");
-  keys.addOutputComponent("pace","FREQUENCY_ADAPTIVE","the hill addition frequency when employing frequency adaptive metadynamics");
-  keys.addOutputComponent("nlker","NLIST","number of hills in the neighbor list");
-  keys.addOutputComponent("nlsteps","NLIST","number of steps from last neighbor list update");
+  keys.addOutputComponent("rct","CALC_RCT","scalar","the reweighting factor c(t).");
+  keys.addOutputComponent("work","CALC_WORK","scalar","accumulator for work");
+  keys.addOutputComponent("acc","ACCELERATION","scalar","the metadynamics acceleration factor");
+  keys.addOutputComponent("maxbias", "CALC_MAX_BIAS", "scalar","the maximum of the metadynamics V(s, t)");
+  keys.addOutputComponent("transbias", "CALC_TRANSITION_BIAS", "scalar","the metadynamics transition bias V*(t)");
+  keys.addOutputComponent("pace","FREQUENCY_ADAPTIVE","scalar","the hill addition frequency when employing frequency adaptive metadynamics");
+  keys.addOutputComponent("nlker","NLIST","scalar","number of hills in the neighbor list");
+  keys.addOutputComponent("nlsteps","NLIST","scalar","number of steps from last neighbor list update");
   keys.use("ARG");
   keys.add("compulsory","SIGMA","the widths of the Gaussian hills");
   keys.add("compulsory","PACE","the frequency for hill addition");

src/bias/MovingRestraint.cpp

@@ -138,17 +138,17 @@ void MovingRestraint::registerKeywords( Keywords& keys ) {
            "parameter is linearly interpolated.  If no KAPPAx is specified for STEPx then the values of KAPPAx "
            "are kept constant during the interval of time between STEP(x-1) and STEPx.");
   keys.reset_style("KAPPA","compulsory");
-  keys.addOutputComponent("work","default","the total work performed changing this restraint");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
-  keys.addOutputComponent("_cntr","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("work","default","scalar","the total work performed changing this restraint");
+  keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("_cntr","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "these quantities will named with  the arguments of the bias followed by "
                           "the character string _cntr. These quantities give the instantaneous position "
                           "of the center of the harmonic potential.");
-  keys.addOutputComponent("_work","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("_work","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "These quantities will named with the arguments of the bias followed by "
                           "the character string _work. These quantities tell the user how much work has "
                           "been done by the potential in dragging the system along the various colvar axis.");
-  keys.addOutputComponent("_kappa","default","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
+  keys.addOutputComponent("_kappa","default","scalar","one or multiple instances of this quantity can be referenced elsewhere in the input file. "
                           "These quantities will named with the arguments of the bias followed by "
                           "the character string _kappa. These quantities tell the user the time dependent value of kappa.");
 }

src/bias/Restraint.cpp

@@ -84,7 +84,7 @@ void Restraint::registerKeywords(Keywords& keys) {
   keys.add("compulsory","SLOPE","0.0","specifies that the restraint is linear and what the values of the force constants on each of the variables are");
   keys.add("compulsory","KAPPA","0.0","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
   keys.add("compulsory","AT","the position of the restraint");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("force2","default","scalar","the instantaneous value of the squared force due to this bias potential");
 }
 
 Restraint::Restraint(const ActionOptions&ao):

src/bias/RestraintShortcut.cpp

@@ -43,8 +43,8 @@ void RestraintShortcut::registerKeywords(Keywords& keys) {
   keys.add("compulsory","KAPPA","0.0","specifies that the restraint is harmonic and what the values of the force constants on each of the variables are");
   keys.add("compulsory","AT","the position of the restraint");
   keys.add("hidden","STRIDE","1","the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms");
-  keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
-  keys.addOutputComponent("force2","default","the instantaneous value of the squared force due to this bias potential");
+  keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
+  keys.addOutputComponent("force2","default","scalar/vector","the instantaneous value of the squared force due to this bias potential");
   keys.addActionNameSuffix("_SCALAR"); keys.needsAction("COMBINE"); keys.needsAction("SUM"); keys.needsAction("CUSTOM"); keys.needsAction("BIASVALUE");
 }