Modified code for creating the dictionary of values that are computed…

… by shortcuts. The names of the actions that have descriptions in the keyword object for a shortcut are now stored at the same time the lines of the shortcut are stored (i.e. when the shortcut actions are created). When driver asks for documentation for these components it thus gets the relevant actions from the shortcut and then looks up the corresponding documentation strings
plumed · May 16, 2024 · 77a52f0 · 77a52f0 · PlumedBot · May 16, 2024
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diff --git a/regtest/basic/rt-parse-only/values.json.reference b/regtest/basic/rt-parse-only/values.json.reference
@@ -23,9 +23,6 @@
 "phi" : { 
 "phi" : { "type": "scalar", "desciption": "" }
 }, 
-"shortcut_phi" : { 
-"phi" : { "type": "scalar", "desciption": "" }
-}, 
 "r1" : { 
 "r1.X" : { "type": "scalar", "description": "values from the column labelled p2.X in the file named input_colvar" } 
 }, 

diff --git a/regtest/contour/rt-parse-only/values.json.reference b/regtest/contour/rt-parse-only/values.json.reference
@@ -29,24 +29,12 @@
 "fcc_mat.y" : { "type": "matrix", "desciption": "" }
 "fcc_mat.z" : { "type": "matrix", "desciption": "" }
 }, 
-"shortcut_fcc_mat" : { 
-"fcc_mat.w" : { "type": "matrix", "desciption": "" }
-"fcc_mat.x" : { "type": "matrix", "desciption": "" }
-"fcc_mat.y" : { "type": "matrix", "desciption": "" }
-"fcc_mat.z" : { "type": "matrix", "desciption": "" }
-}, 
 "fcc_vfunc" : { 
 "fcc_vfunc" : { "type": "matrix", "desciption": "" }
 }, 
-"shortcut_fcc_vfunc" : { 
-"fcc_vfunc" : { "type": "matrix", "desciption": "" }
-}, 
 "fcc_wvfunc" : { 
 "fcc_wvfunc" : { "type": "matrix", "desciption": "" }
 }, 
-"shortcut_fcc_wvfunc" : { 
-"fcc_wvfunc" : { "type": "matrix", "desciption": "" }
-}, 
 "fcc_ones" : { 
 "fcc_ones" : { "type": "vector", "desciption": "" }
 }, 
@@ -62,8 +50,8 @@
 "fcc_n" : { 
 "fcc_n" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_fcc_n" : { 
-"fcc_n" : { "type": "vector", "desciption": "" }
+"shortcut_fcc" : { 
+"fcc" : { "type": "vector", "desciption": "" }
 }, 
 "dens_dist" : { 
 "dens_dist.x" : { "type": "vector", "desciption": "" }
@@ -81,15 +69,9 @@
 "dens_numer_cov" : { 
 "dens_numer_cov" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dens_numer_cov" : { 
-"dens_numer_cov" : { "type": "vector", "desciption": "" }
-}, 
 "dens_numer_icov" : { 
 "dens_numer_icov" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dens_numer_icov" : { 
-"dens_numer_icov" : { "type": "vector", "desciption": "" }
-}, 
 "dens_numer" : { 
 "dens_numer" : { "type": "grid", "desciption": "" }
 }, 
@@ -105,24 +87,15 @@
 "dens_denom_cov" : { 
 "dens_denom_cov" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dens_denom_cov" : { 
-"dens_denom_cov" : { "type": "vector", "desciption": "" }
-}, 
 "dens_denom_icov" : { 
 "dens_denom_icov" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dens_denom_icov" : { 
-"dens_denom_icov" : { "type": "vector", "desciption": "" }
-}, 
 "dens_denom" : { 
 "dens_denom" : { "type": "grid", "desciption": "" }
 }, 
 "dens" : { 
 "dens" : { "type": "grid", "desciption": "" }
 }, 
-"shortcut_dens" : { 
-"dens" : { "type": "grid", "desciption": "" }
-}, 
 "cont" : { 
 "cont.dens_dist.x" : { "type": "vector", "description": "a vector of coordinates for the contour along the dens_dist.x direction" }, 
 "cont.dens_dist.y" : { "type": "vector", "description": "a vector of coordinates for the contour along the dens_dist.y direction" }, 

diff --git a/regtest/multicolvar/rt-parse-only/config b/regtest/multicolvar/rt-parse-only/config
@@ -2,5 +2,5 @@ type=driver
 # this is to test automatic sizing  
 arg="--parse-only --natoms 10000 --shortcut-ofile shortcuts.json --valuedict-ofile values_pre.json"
 function plumed_regtest_after(){
-  cat values_pre.json | awk '{ for(i=1;i<=NF;++i){ if($i=="\"description\":") { if(match($1, /[1-9]/)) printf("\"desciption\": \"%s\" }", $(i+2)); else printf("\"desciption\": \"\" }"); break; } printf "%s ", $i }; printf("\n");}' > values.json
+  cat values_pre.json | awk '{ for(i=1;i<=NF;++i){ if($i=="\"description\":") { if(match($1, /[1-9]/) && match($(i+2), /[1-9]/)) printf("\"desciption\": \"%s\" }", $(i+2)); else printf("\"desciption\": \"\" }"); break; } printf "%s ", $i }; printf("\n");}' > values.json
 }
diff --git a/regtest/multicolvar/rt-parse-only/plumed.dat b/regtest/multicolvar/rt-parse-only/plumed.dat
@@ -8,3 +8,5 @@ ssall: SORT ARG=dall
 
 dallt: DISTANCE ATOMS1=7,8 ATOMS2=9,10 ATOMS3=11,12
 sfinal: SORT ARG=dall,dallt
+
+dallk: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 MEAN LESS_THAN1={RATIONAL R_0=1.0} LESS_THAN2={RATIONAL R_0=1.5} LOWEST
diff --git a/regtest/multicolvar/rt-parse-only/shortcuts.json.reference b/regtest/multicolvar/rt-parse-only/shortcuts.json.reference
@@ -0,0 +1,5 @@
+{
+   "dallk" : {
+      "expansion" : "dallk_vatom1: CENTER ATOMS=1,2\ndallk_vatom2: CENTER ATOMS=3,4\ndallk_vatom3: CENTER ATOMS=5,6\ndallk_grp: GROUP ATOMS=dallk_vatom1,dallk_vatom2,dallk_vatom3\ndallk: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6\ndallk_lt1: LESS_THAN ARG=dallk SWITCH={RATIONAL R_0=1.0}\ndallk_lessthan-1: SUM ARG=dallk_lt1 PERIODIC=NO\ndallk_lt2: LESS_THAN ARG=dallk SWITCH={RATIONAL R_0=1.5}\ndallk_lessthan-2: SUM ARG=dallk_lt2 PERIODIC=NO\ndallk_lowest: LOWEST ARG=dallk\ndallk_mean: MEAN ARG=dallk PERIODIC=NO"
+   }
+}
diff --git a/regtest/multicolvar/rt-parse-only/values.json.reference b/regtest/multicolvar/rt-parse-only/values.json.reference
@@ -21,61 +21,72 @@
 "Box" : { "type": "matrix", "desciption": "" }
 }, 
 "d1" : { 
-"d1" : { "type": "scalar", "desciption": "DISTANCE" }
-}, 
-"shortcut_d1" : { 
-"d1" : { "type": "scalar", "desciption": "DISTANCE" }
+"d1" : { "type": "scalar", "desciption": "" }
 }, 
 "d2" : { 
-"d2" : { "type": "scalar", "desciption": "DISTANCE" }
-}, 
-"shortcut_d2" : { 
-"d2" : { "type": "scalar", "desciption": "DISTANCE" }
+"d2" : { "type": "scalar", "desciption": "" }
 }, 
 "d3" : { 
-"d3" : { "type": "scalar", "desciption": "DISTANCE" }
-}, 
-"shortcut_d3" : { 
-"d3" : { "type": "scalar", "desciption": "DISTANCE" }
+"d3" : { "type": "scalar", "desciption": "" }
 }, 
 "ss" : { 
 "ss.1" : { "type": "scalar", "desciption": "1th" }
 "ss.2" : { "type": "scalar", "desciption": "2th" }
 "ss.3" : { "type": "scalar", "desciption": "3th" }
 }, 
-"shortcut_ss" : { 
-"ss.1" : { "type": "scalar", "desciption": "1th" }
-"ss.2" : { "type": "scalar", "desciption": "2th" }
-"ss.3" : { "type": "scalar", "desciption": "3th" }
-}, 
 "dall" : { 
 "dall" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dall" : { 
-"dall" : { "type": "vector", "desciption": "" }
-}, 
 "ssall" : { 
 "ssall.1" : { "type": "scalar", "desciption": "1th" }
 "ssall.2" : { "type": "scalar", "desciption": "2th" }
 "ssall.3" : { "type": "scalar", "desciption": "3th" }
 }, 
-"shortcut_ssall" : { 
-"ssall.1" : { "type": "scalar", "desciption": "1th" }
-"ssall.2" : { "type": "scalar", "desciption": "2th" }
-"ssall.3" : { "type": "scalar", "desciption": "3th" }
-}, 
 "dallt" : { 
 "dallt" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_dallt" : { 
-"dallt" : { "type": "vector", "desciption": "" }
-}, 
 "sfinal" : { 
 "sfinal.1" : { "type": "scalar", "desciption": "1th" }
 "sfinal.2" : { "type": "scalar", "desciption": "2th" }
 }, 
-"shortcut_sfinal" : { 
-"sfinal.1" : { "type": "scalar", "desciption": "1th" }
-"sfinal.2" : { "type": "scalar", "desciption": "2th" }
+"dallk_vatom1" : { 
+"dallk_vatom1" : { "type": "atoms", "desciption": "" }
+}, 
+"dallk_vatom2" : { 
+"dallk_vatom2" : { "type": "atoms", "desciption": "" }
+}, 
+"dallk_vatom3" : { 
+"dallk_vatom3" : { "type": "atoms", "desciption": "" }
+}, 
+"dallk_grp" : { 
+"dallk_grp" : { "type": "atoms", "desciption": "" }
+}, 
+"dallk" : { 
+"dallk" : { "type": "vector", "desciption": "" }
+}, 
+"dallk_lt1" : { 
+"dallk_lt1" : { "type": "vector", "desciption": "" }
+}, 
+"dallk_lessthan-1" : { 
+"dallk_lessthan-1" : { "type": "scalar", "desciption": "" }
+}, 
+"dallk_lt2" : { 
+"dallk_lt2" : { "type": "vector", "desciption": "" }
+}, 
+"dallk_lessthan-2" : { 
+"dallk_lessthan-2" : { "type": "scalar", "desciption": "" }
+}, 
+"dallk_lowest" : { 
+"dallk_lowest" : { "type": "scalar", "desciption": "" }
+}, 
+"dallk_mean" : { 
+"dallk_mean" : { "type": "scalar", "desciption": "" }
+}, 
+"shortcut_dallk" : { 
+"dallk" : { "type": "vector", "desciption": "" }
+"dallk_lessthan-1" : { "type": "scalar", "desciption": "" }
+"dallk_lessthan-2" : { "type": "scalar", "desciption": "" }
+"dallk_lowest" : { "type": "scalar", "desciption": "" }
+"dallk_mean" : { "type": "scalar", "desciption": "" }
 } 
 } 
diff --git a/regtest/symfunc/rt-parse-only/values.json.reference b/regtest/symfunc/rt-parse-only/values.json.reference
@@ -29,12 +29,6 @@
 "q1_mat.y" : { "type": "matrix", "desciption": "" }
 "q1_mat.z" : { "type": "matrix", "desciption": "" }
 }, 
-"shortcut_q1_mat" : { 
-"q1_mat.w" : { "type": "matrix", "desciption": "" }
-"q1_mat.x" : { "type": "matrix", "desciption": "" }
-"q1_mat.y" : { "type": "matrix", "desciption": "" }
-"q1_mat.z" : { "type": "matrix", "desciption": "" }
-}, 
 "q1_sh" : { 
 "q1_sh.rm-n1" : { "type": "matrix", "desciption": "" }
 "q1_sh.rm-0" : { "type": "matrix", "desciption": "" }
@@ -63,15 +57,9 @@
 "q1_norm2" : { 
 "q1_norm2" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_q1_norm2" : { 
-"q1_norm2" : { "type": "vector", "desciption": "" }
-}, 
 "q1_norm" : { 
 "q1_norm" : { "type": "vector", "desciption": "" }
 }, 
-"shortcut_q1_norm" : { 
-"q1_norm" : { "type": "vector", "desciption": "" }
-}, 
 "q1" : { 
 "q1" : { "type": "vector", "desciption": "" }
 }, 

diff --git a/regtest/wham/rt-parse-only/values.json.reference b/regtest/wham/rt-parse-only/values.json.reference
@@ -23,9 +23,6 @@
 "phi" : { 
 "phi" : { "type": "scalar", "desciption": "" }
 }, 
-"shortcut_phi" : { 
-"phi" : { "type": "scalar", "desciption": "" }
-}, 
 "rp" : { 
 "rp.bias" : { "type": "scalar", "desciption": "" }
 "rp.force2" : { "type": "scalar", "desciption": "" }

diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
@@ -804,30 +804,33 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
           }
           ActionShortcut* as=pp->castToActionShortcut();
           if( as ) {
-            unsigned ncomponents = 0; std::vector<ActionWithValue*> val_actions;
-            Keywords keys; actionRegister().getKeywords( as->getName(), keys );
-            std::vector<std::string> cnames( keys.getOutputComponents() );
-            for(unsigned i=0; i<cnames.size(); ++i) {
-              std::string valname;
-              if( cnames[i]==".#!value" ) valname = as->getShortcutLabel();
-              else valname = as->getShortcutLabel() + "_" + cnames[i];
-              ActionWithValue* av = p.getActionSet().selectWithLabel<ActionWithValue*>( valname );
-              if( av ) val_actions.push_back(av);
-            }
-            if( val_actions.size()==0 ) continue ;
+            std::vector<std::string> cnames( as->getSavedOutputs() );
+            printf("CHECK %s %s %d \n", as->getShortcutLabel().c_str(), as->getName().c_str(), cnames.size() );
+            if( cnames.size()==0 ) continue ;
 
             if( firsta ) { valuefile.printf("  \"shortcut_%s\" : {\n", as->getShortcutLabel().c_str() ); firsta=false; }
             else valuefile.printf(",\n  \"shortcut_%s\" : {\n", as->getShortcutLabel().c_str() );
-            bool firstv=true;
-            for(unsigned i=0; i<val_actions.size(); ++i) {
-              for(unsigned j=0; j<val_actions[i]->getNumberOfComponents(); ++j) {
-                Value* myval = val_actions[i]->copyOutput(j); std::string compname = myval->getName(), description; std::size_t dot=compname.find(".");
-                if( dot!=std::string::npos ) {
-                  std::string cname = compname.substr(dot+1); description = val_actions[i]->getOutputComponentDescription( cname, keys );
-                } else description = keys.getOutputComponentDescription(".#!value");
-                if( description.find("\\")!=std::string::npos ) error("found invalid backslash character in documentation for component " + compname + " in action " + val_actions[i]->getName() + " with label " + val_actions[i]->getLabel() );
+            bool firstv=true; Keywords keys; actionRegister().getKeywords( as->getName(), keys );
+            for(unsigned i=0; i<cnames.size(); ++i) {
+              ActionWithValue* av2=p.getActionSet().selectWithLabel<ActionWithValue*>( cnames[i] );
+              if( !av2 ) plumed_merror("could not find value created by shortcut with name " + cnames[i] );
+              if( av2->getNumberOfComponents()==1 ) {
+                Value* myval = av2->copyOutput(0); std::string compname = myval->getName(), description;
+                if( compname==as->getShortcutLabel() ) description = keys.getOutputComponentDescription(".#!value");
+                else { std::size_t pp=compname.find(as->getShortcutLabel()); description = keys.getOutputComponentDescription( compname.substr(pp+as->getShortcutLabel().length()+1) ); }
+                if( description.find("\\")!=std::string::npos ) error("found invalid backslash character in documentation for component " + compname + " in action " + as->getName() + " with label " + as->getLabel() );
                 if( firstv ) { valuefile.printf("    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() ); firstv=false; }
                 else valuefile.printf(",\n    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() );
+              } else {
+                for(unsigned j=0; j<av2->getNumberOfComponents(); ++j) {
+                  Value* myval = av2->copyOutput(j); std::string compname = myval->getName(), description; std::size_t dot=compname.find(".");
+                  if( dot!=std::string::npos ) {
+                    std::string cname = compname.substr(dot+1); description = av2->getOutputComponentDescription( cname, keys );
+                  } else plumed_merror("should not be outputting description of value from action when using shortcuts");
+                  if( description.find("\\")!=std::string::npos ) error("found invalid backslash character in documentation for component " + compname + " in action " + av2->getName() + " with label " + av2->getLabel() );
+                  if( firstv ) { valuefile.printf("    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() ); firstv=false; }
+                  else valuefile.printf(",\n    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() );
+                }
               }
             }
             valuefile.printf("\n  }");

diff --git a/src/core/ActionShortcut.cpp b/src/core/ActionShortcut.cpp
@@ -83,6 +83,28 @@ void ActionShortcut::readInputLine( const std::string& input ) {
       if( !restart ) f_input += " RESTART=NO";
     }
     plumed.readInputLine( f_input );
+    if( !founds ) {
+      ActionWithValue* av=NULL;
+      for(auto pp=plumed.getActionSet().rbegin(); pp!=plumed.getActionSet().rend(); ++pp) {
+        av = pp->get()->castToActionWithValue();
+        if( !av ) continue ;
+        if( std::find(savedOutputs.begin(), savedOutputs.end(), av->getLabel() )!=savedOutputs.end() ) av=NULL;
+        break;
+      }
+      if( av ) {
+        std::string av_label = av->getLabel();
+        if( av_label == getShortcutLabel() ) savedOutputs.push_back( av_label );
+        else {
+          for(unsigned i=0; i<keywords.cnames.size(); ++i) {
+            if( av_label == getShortcutLabel() + "_" + keywords.cnames[i] ) savedOutputs.push_back( av_label );
+            else if( keywords.getOutputComponentFlag(keywords.cnames[i])!="default" ) {
+              std::string thisflag = keywords.getOutputComponentFlag(keywords.cnames[i]);
+              if( keywords.numbered(thisflag) && av_label.find(getShortcutLabel() + "_" + keywords.cnames[i])!=std::string::npos ) savedOutputs.push_back( av_label );
+            }
+          }
+        }
+      }
+    }
   } else error("requirement for action " + words[0] + " should be registered in registerKeywords function for shortcut action using keys.useAction");
 }
 
@@ -105,6 +127,10 @@ std::vector<std::string> ActionShortcut::getSavedInputLines() const {
   return savedInputLines;
 }
 
+std::vector<std::string> ActionShortcut::getSavedOutputs() const {
+  return savedOutputs;
+}
+
 std::string ActionShortcut::convertInputLineToString() {
   std::string output;
   for(auto p=line.begin(); p!=line.end(); ++p) {

diff --git a/src/core/ActionShortcut.h b/src/core/ActionShortcut.h
@@ -36,6 +36,7 @@ class ActionShortcut :
 private:
   std::string shortcutlabel;
   std::vector<std::string> savedInputLines;
+  std::vector<std::string> savedOutputs;
 protected:
   std::string getUpdateLimits() const ;
 public:
@@ -53,6 +54,8 @@ class ActionShortcut :
   void apply() override {}
 /// Get the lines of the shortcut that were read in
   std::vector<std::string> getSavedInputLines() const ;
+/// Get the labels of the actions that this creates
+  std::vector<std::string> getSavedOutputs() const ;
 /// Take everything that was input to this action and convert it to a string
   std::string convertInputLineToString();
 /// This sorts out the reading of arguments from shortcuts

diff --git a/src/symfunc/CoordinationNumbers.cpp b/src/symfunc/CoordinationNumbers.cpp
@@ -145,7 +145,7 @@ void CoordinationNumbers::registerKeywords( Keywords& keys ) {
   keys.add("compulsory","R_POWER","the power to which you want to raise the distance");
   keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");
   keys.add("optional","MOMENTS","the list of moments that you would like to calculate");
-  keys.addOutputComponent("moment","MOMENT","the moments of the distribution");
+  keys.addOutputComponent("moment","MOMENTS","the moments of the distribution");
   keys.needsAction("MATRIX_VECTOR_PRODUCT"); keys.needsAction("ONES"); keys.needsAction("MOMENTS");
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,3 +8,5 @@ ssall: SORT ARG=dall

		dallt: DISTANCE ATOMS1=7,8 ATOMS2=9,10 ATOMS3=11,12
		sfinal: SORT ARG=dall,dallt

		dallk: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 MEAN LESS_THAN1={RATIONAL R_0=1.0} LESS_THAN2={RATIONAL R_0=1.5} LOWEST