More fixes to resolve problems with inputs in nest

-> Changed label for list of q6 values to <shortcut_label> rather than <shortcut_label>_anorm.  This is clearer
-> Implemented UWALLS shortcut.  It just calls UPPER_WALLS.
-> Made ARG compulsory keyword for CLUSTER_PROPERTIES.
-> Creating GROUP of atoms in Distances and LOCAL_Q? so folks can use the label of the action to refer to the atom involved a la multicolvar

Also fixed a few things that I didn't implement correctly in the last commit

regtest/contour/rt-dfg-wcsurf/plumed.dat

@@ -9,7 +9,7 @@ dp_mat: OUTER_PRODUCT ARG=cf,cf
 mat: CUSTOM ARG=c1_mat2,dp_mat FUNC=x*y PERIODIC=NO
 # Find largest cluster
 dfs: DFSCLUSTERING ARG=mat 
-clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 
+clust1: CLUSTER_WEIGHTS CLUSTERS=dfs CLUSTER=1 
 nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
 
 # Print out the size of the cluster and the atoms

regtest/gridtools/rt-q6-histogram/density.reference

@@ -1,12 +1,12 @@
-#! FIELDS c1 q6_anorm h dh_c1 dh_q6_anorm
+#! FIELDS c1 q6 h dh_c1 dh_q6
 #! SET min_c1 0
 #! SET max_c1 10
 #! SET nbins_c1  200
 #! SET periodic_c1 false
-#! SET min_q6_anorm 0
-#! SET max_q6_anorm 2
-#! SET nbins_q6_anorm  200
-#! SET periodic_q6_anorm false
+#! SET min_q6 0
+#! SET max_q6 2
+#! SET nbins_q6  200
+#! SET periodic_q6 false
    0.0000   0.0000   0.0000   0.0000   0.0000
    0.0500   0.0000   0.0000   0.0002   0.0002
    0.1000   0.0000   0.0000   0.0011   0.0011

regtest/gridtools/rt-q6-histogram/plumed.dat

@@ -1,4 +1,4 @@
 c1: COORDINATIONNUMBER SPECIESA=1,2 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
 q6: Q6 SPECIESA=1,2 SPECIESB=1-200 SWITCH={RATIONAL R_0=1.0}
-h: HISTOGRAM ARG=c1,q6_anorm GRID_BIN=200,200 GRID_MIN=0,0 GRID_MAX=10,2 BANDWIDTH=0.1,0.1 
+h: HISTOGRAM ARG=c1,q6 GRID_BIN=200,200 GRID_MIN=0,0 GRID_MAX=10,2 BANDWIDTH=0.1,0.1 
 DUMPGRID ARG=h STRIDE=20 FILE=density FMT=%8.4f

regtest/symfunc/rt-dumpmulti/plumed.dat

@@ -30,7 +30,7 @@ q6n_imn-[4]: CUSTOM ARG=q6_sp.im-p4,q6_norm FUNC=x/y PERIODIC=NO
 q6n_imn-[5]: CUSTOM ARG=q6_sp.im-p5,q6_norm FUNC=x/y PERIODIC=NO
 q6n_imn-[6]: CUSTOM ARG=q6_sp.im-p6,q6_norm FUNC=x/y PERIODIC=NO
 
-DUMPATOMS ATOMS=q6 ARG=q6_anorm,q6n_rmn-[-6],q6n_rmn-[-5],q6n_rmn-[-4],q6n_rmn-[-3],q6n_rmn-[-2],q6n_rmn-[-1],q6n_rmn-[0],q6n_rmn-[1],q6n_rmn-[2],q6n_rmn-[3],q6n_rmn-[4],q6n_rmn-[5],q6n_rmn-[6],q6n_imn-[-6],q6n_imn-[-5],q6n_imn-[-4],q6n_imn-[-3],q6n_imn-[-2],q6n_imn-[-1],q6n_imn-[0],q6n_imn-[1],q6n_imn-[2],q6n_imn-[3],q6n_imn-[4],q6n_imn-[5],q6n_imn-[6] FILE=q6.xyz PRECISION=4
+DUMPATOMS ATOMS=q6 ARG=q6,q6n_rmn-[-6],q6n_rmn-[-5],q6n_rmn-[-4],q6n_rmn-[-3],q6n_rmn-[-2],q6n_rmn-[-1],q6n_rmn-[0],q6n_rmn-[1],q6n_rmn-[2],q6n_rmn-[3],q6n_rmn-[4],q6n_rmn-[5],q6n_rmn-[6],q6n_imn-[-6],q6n_imn-[-5],q6n_imn-[-4],q6n_imn-[-3],q6n_imn-[-2],q6n_imn-[-1],q6n_imn-[0],q6n_imn-[1],q6n_imn-[2],q6n_imn-[3],q6n_imn-[4],q6n_imn-[5],q6n_imn-[6] FILE=q6.xyz PRECISION=4
 
 w6: LOCAL_Q6 SPECIES=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN 
 DUMPATOMS ARG=w6_av ATOMS=q6 FILE=w6.xyz PRECISION=4

regtest/symfunc/rt24/colvar2.reference

@@ -1,6 +1,6 @@
-#! FIELDS time c2_moment-2 c2_moment-3 c2_lessthan-1 c2_lessthan-2
- 0.000000   0.0383  -0.0032   0.0005   0.0019
- 0.005000   0.0427  -0.0041   0.0006   0.0023
- 0.010000   0.0585  -0.0020   0.0008   0.0029
- 0.015000   0.0778   0.0037   0.0011   0.0040
- 0.020000   0.0707   0.0027   0.0014   0.0052
+#! FIELDS time c2_lessthan-1 c2_lessthan-2 c2_moment-2 c2_moment-3
+ 0.000000   0.0005   0.0019   0.0383  -0.0032
+ 0.005000   0.0006   0.0023   0.0427  -0.0041
+ 0.010000   0.0008   0.0029   0.0585  -0.0020
+ 0.015000   0.0011   0.0040   0.0778   0.0037
+ 0.020000   0.0014   0.0052   0.0707   0.0027

regtest/symfunc/rt24/plumed.dat

@@ -4,4 +4,4 @@ PRINT ARG=mom.* FILE=colvar FMT=%8.4f
 BIASVALUE ARG=mom.* 
 
 c2: COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0} MOMENTS=2-3 LESS_THAN1={RATIONAL R_0=0.2} LESS_THAN2={RATIONAL R_0=0.25}
-PRINT ARG=c2.moment-2,c2.moment-3,c2.* FILE=colvar2 FMT=%8.4f 
+PRINT ARG=c2.* FILE=colvar2 FMT=%8.4f 

regtest/volumes/rt-q3-insphere/plumed.dat

@@ -9,7 +9,7 @@ q3: Q3 SPECIES=ow SWITCH={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34}
 
 # Probe volume
 sphere: INSPHERE ATOMS=q3 CENTER=center RADIUS={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52}
-prod: CUSTOM ARG=q3_anorm,sphere FUNC=x*y PERIODIC=NO
+prod: CUSTOM ARG=q3,sphere FUNC=x*y PERIODIC=NO
 sphere_sum: SUM ARG=prod PERIODIC=NO
 
 # Bias the mean value of the OP in the sphere

src/clusters/ClusterProperties.cpp

@@ -66,7 +66,7 @@ PLUMED_REGISTER_ACTION(ClusterProperties,"CLUSTER_PROPERTIES")
 
 void ClusterProperties::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
-  keys.add("optional","ARG","calculate the sum of the arguments calculated by this action for the cluster");
+  keys.add("compulsory","ARG","calculate the sum of the arguments calculated by this action for the cluster");
   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
   keys.add("compulsory","CLUSTER","1","which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.");
   multicolvar::MultiColvarShortcuts::shortcutKeywords( keys );

src/core/Action.cpp

@@ -254,7 +254,7 @@ void Action::setupConstantValues( const bool& have_atoms ) {
     }
   }
   ActionWithArguments* aa = castToActionWithArguments();
-  if( aa && aa->getNumberOfArguments()>0 ) never_activate = aa->calculateConstantValues( have_atoms );
+  if( aa && aa->getNumberOfArguments()>0 && getName()!="BIASVALUE" ) never_activate = aa->calculateConstantValues( have_atoms );
 }
 
 long long int Action::getStep()const {

src/core/ActionShortcut.cpp

@@ -137,8 +137,9 @@ void ActionShortcut::interpretDataLabel( const std::string& mystr, Action* myuse
           for(unsigned j=1;; ++j) {
             std::string numstr; Tools::convert( j, numstr );
             ActionWithValue* act=plumed.getActionSet().selectWithLabel<ActionWithValue*>( a + "_" + out_comps[k] + "-" + numstr );
-            if(!act) break;
-            for(unsigned n=0; n<act->getNumberOfComponents(); ++n ) arg.push_back(act->copyOutput(n));
+            if( act ) {
+              for(unsigned n=0; n<act->getNumberOfComponents(); ++n ) arg.push_back(act->copyOutput(n));
+            } else if( j>1 ) break;    // This ensures that * syntax works with moments, which normally start from 2
           }
         }
       }

src/multicolvar/Angles.cpp

@@ -120,7 +120,7 @@ Angles::Angles(const ActionOptions&ao):
   if( swit.length()>0 ) {
     std::string cat, grp; parse("GROUPA",cat); parse("GROUPB",grp);
     if( cat.length()==0 || grp.length()==0 ) error("must use GROUPA/GROUPB when using SWITCH");
-    readInputLine( getShortcutLabel() + ": COORD_ANGLES SWITCH={" +  swit + "} CATOMS=" + cat + " GROUP=" + grp );
+    readInputLine( getShortcutLabel() + ": COORD_ANGLES SWITCH={" +  swit + "} CATOMS=" + cat + " GROUP=" + grp + " " + convertInputLineToString() );
     return;
   }
   std::vector<std::string> group; parseVector("GROUP",group);

src/multicolvar/Distances.cpp

@@ -246,12 +246,16 @@ Distances::Distances(const ActionOptions& ao):
     } else if( grpa.size()>0 ) {
       std::vector<std::string> grpb; MultiColvarShortcuts::parseAtomList("GROUPB",grpb,this);
       if( grpb.size()==0 ) error("found GROUPA but no corresponding GROUPB");
+      std::string grpstr = getShortcutLabel() + "_grp: GROUP ATOMS=";
       for(unsigned i=0; i<grpa.size(); ++i) {
         for(unsigned j=0; j<grpb.size(); ++j) {
           std::string num; Tools::convert( i*grpb.size() + j + 1, num );
           dline += " ATOMS" + num + "=" + grpa[i] + "," + grpb[j];
+          readInputLine( getShortcutLabel() + "_vatom" + num + ": CENTER ATOMS=" + grpa[i] + "," + grpb[j] );
+          if( i+j==0 ) grpstr += getShortcutLabel() + "_vatom" + num; else grpstr += "," + getShortcutLabel() + "_vatom" + num;
         }
       }
+      readInputLine( grpstr );
     } else {
       std::string grpstr = getShortcutLabel() + "_grp: GROUP ATOMS=";
       for(unsigned i=1;; ++i) {

src/multicolvar/MFilterLess.cpp

@@ -49,7 +49,7 @@ void MFilterLess::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
   keys.add("compulsory","DATA","the vector you wish to transform");
   keys.add("compulsory","SWITCH","the switching function that transform");
-  keys.needsAction("GROUP"); keys.needsAction("MORE_THAN");
+  keys.needsAction("GROUP"); keys.needsAction("LESS_THAN");
 }
 
 MFilterLess::MFilterLess(const ActionOptions& ao):

src/multicolvar/MFilterMore.cpp

@@ -52,7 +52,8 @@ void MFilterMore::registerKeywords(Keywords& keys) {
   keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");
   keys.addFlag("HIGHEST",false,"this flag allows you to recover the highest of these variables.");
   keys.addOutputComponent("highest","HIGHEST","the largest of the colvars");
-  keys.needsAction("CUSTOM"); keys.needsAction("GROUP"); keys.needsAction("MORE_THAN");
+  keys.needsAction("CUSTOM"); keys.needsAction("GROUP");
+  keys.needsAction("MORE_THAN"); keys.needsAction("HIGHEST");
 }
 
 MFilterMore::MFilterMore(const ActionOptions& ao):

src/multicolvar/UWalls.cpp

@@ -0,0 +1,74 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2018 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "core/ActionShortcut.h"
+#include "core/ActionRegister.h"
+#include "MultiColvarShortcuts.h"
+
+//+PLUMEDOC MCOLVAR UWALLS
+/*
+Add lower walls to a vector of quantities
+
+Depracated action: use UPPER_WALLS
+
+\par Examples
+
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace multicolvar {
+
+class UWalls : public ActionShortcut {
+public:
+  static void registerKeywords(Keywords& keys);
+  explicit UWalls(const ActionOptions&);
+};
+
+PLUMED_REGISTER_ACTION(UWalls,"UWALLS")
+
+void UWalls::registerKeywords(Keywords& keys) {
+  ActionShortcut::registerKeywords( keys );
+  keys.add("compulsory","DATA","the values you want to restrain");
+  keys.add("compulsory","AT","the radius of the sphere");
+  keys.add("compulsory","KAPPA","the force constant for the wall.  The k_i in the expression for a wall.");
+  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.add("atoms","CATOMS","all the angles between the bonds that radiate out from these central atom are computed");
+  keys.add("atoms","GROUP","a list of angls between pairs of bonds connecting one of the atoms specified using the CATOM command and two of the atoms specified here are computed");
+  keys.add("compulsory","SWITCH","the switching function specifies that only those bonds that have a length that is less than a certain threshold are considered");
+  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.needsAction("UPPER_WALLS");
+}
+
+UWalls::UWalls(const ActionOptions& ao):
+  Action(ao),
+  ActionShortcut(ao)
+{
+  std::string data; parse("DATA",data);
+  readInputLine( getShortcutLabel() + ": UPPER_WALLS ARG=" + data + " " + convertInputLineToString() );
+}
+
+}
+}

src/symfunc/LocalSteinhardt.cpp

@@ -293,7 +293,7 @@ void LocalSteinhardt::registerKeywords( Keywords& keys ) {
            "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
   keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");
   multicolvar::MultiColvarShortcuts::shortcutKeywords( keys );
-  keys.needsAction("CONTACT_MATRIX"); keys.needsAction("MATRIX_PRODUCT");
+  keys.needsAction("CONTACT_MATRIX"); keys.needsAction("MATRIX_PRODUCT"); keys.needsAction("GROUP");
   keys.needsAction("ONES"); keys.needsAction("OUTER_PRODUCT"); keys.needsAction("VSTACK");
   keys.needsAction("CONCATENATE"); keys.needsAction("CUSTOM"); keys.needsAction("TRANSPOSE");
   keys.needsAction("MATRIX_VECTOR_PRODUCT");
@@ -335,6 +335,8 @@ LocalSteinhardt::LocalSteinhardt(const ActionOptions& ao):
   std::string sp_str; parse("SPECIES",sp_str);
   std::string spa_str; parse("SPECIESA",spa_str);
   if( sp_str.length()>0 ) {
+    // Create a group with these atoms
+    readInputLine( getShortcutLabel() + "_grp: GROUP ATOMS=" + sp_str );
     std::vector<std::string> sp_lab = Tools::getWords(sp_str, "\t\n ,");
     // This creates the stash to hold all the vectors
     if( sp_lab.size()==1 ) {
@@ -366,6 +368,8 @@ LocalSteinhardt::LocalSteinhardt(const ActionOptions& ao):
     // And the matrix of dot products
     readInputLine( getShortcutLabel() + "_dpmat: MATRIX_PRODUCT ARG=" + getShortcutLabel() + "_vecs," + getShortcutLabel() + "_vecsT" );
   } else if( spa_str.length()>0 ) {
+    // Create a group with these atoms
+    readInputLine( getShortcutLabel() + "_grp: GROUP ATOMS=" + spa_str );
     std::string spb_str; parse("SPECIESB",spb_str);
     if( spb_str.length()==0 ) plumed_merror("need both SPECIESA and SPECIESB in input");
     std::vector<std::string> sp_laba = Tools::getWords(spa_str, "\t\n ,");

src/symfunc/Steinhardt.cpp

@@ -360,8 +360,8 @@ Steinhardt::Steinhardt( const ActionOptions& ao):
   // Now calculate the total length of the vector
   createVectorNormInput( getShortcutLabel() + "_sp", getShortcutLabel() + "_norm", l, ".", "m" );
   // And take average
-  readInputLine( getShortcutLabel() + "_anorm: CUSTOM ARG=" + getShortcutLabel() + "_norm," + getShortcutLabel() + "_denom FUNC=x/y PERIODIC=NO");
-  multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel() + "_anorm", "", this );
+  readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_norm," + getShortcutLabel() + "_denom FUNC=x/y PERIODIC=NO");
+  multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
 }
 
 void Steinhardt::createVectorNormInput( const std::string& ilab, const std::string& olab, const int& l, const std::string& sep, const std::string& vlab ) {