Added documentation for stuff represented by shortcut labels to value…

…dict files that are output by driver with the --valuedict-ofile option This is a feature that is used by the nest
plumed · May 15, 2024 · 55443b5 · 55443b5 · PlumedBot · May 15, 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
@@ -23,6 +23,9 @@
 "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
@@ -29,15 +29,30 @@
 "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": "" }
 }, 
+"shortcut_fcc_ones" : { 
+"fcc_ones" : { "type": "vector", "desciption": "" }
+}, 
 "fcc" : { 
 "fcc" : { "type": "vector", "desciption": "" }
 }, 
@@ -47,41 +62,67 @@
 "fcc_n" : { 
 "fcc_n" : { "type": "vector", "desciption": "" }
 }, 
+"shortcut_fcc_n" : { 
+"fcc_n" : { "type": "vector", "desciption": "" }
+}, 
 "dens_dist" : { 
 "dens_dist.x" : { "type": "vector", "desciption": "" }
 "dens_dist.y" : { "type": "vector", "desciption": "" }
 "dens_dist.z" : { "type": "vector", "desciption": "" }
 }, 
+"shortcut_dens_dist" : { 
+"dens_dist.x" : { "type": "vector", "desciption": "" }
+"dens_dist.y" : { "type": "vector", "desciption": "" }
+"dens_dist.z" : { "type": "vector", "desciption": "" }
+}, 
 "dens_numer_sigma" : { 
 "dens_numer_sigma" : { "type": "vector", "desciption": "" }
 }, 
 "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": "" }
 }, 
 "ones" : { 
 "ones" : { "type": "vector", "desciption": "" }
 }, 
+"shortcut_ones" : { 
+"ones" : { "type": "vector", "desciption": "" }
+}, 
 "dens_denom_sigma" : { 
 "dens_denom_sigma" : { "type": "vector", "desciption": "" }
 }, 
 "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/values.json.reference b/regtest/multicolvar/rt-parse-only/values.json.reference
@@ -23,30 +23,59 @@
 "d1" : { 
 "d1" : { "type": "scalar", "desciption": "DISTANCE" }
 }, 
+"shortcut_d1" : { 
+"d1" : { "type": "scalar", "desciption": "DISTANCE" }
+}, 
 "d2" : { 
 "d2" : { "type": "scalar", "desciption": "DISTANCE" }
 }, 
+"shortcut_d2" : { 
+"d2" : { "type": "scalar", "desciption": "DISTANCE" }
+}, 
 "d3" : { 
 "d3" : { "type": "scalar", "desciption": "DISTANCE" }
 }, 
+"shortcut_d3" : { 
+"d3" : { "type": "scalar", "desciption": "DISTANCE" }
+}, 
 "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" }
 } 
 } 
diff --git a/regtest/wham/rt-parse-only/values.json.reference b/regtest/wham/rt-parse-only/values.json.reference
@@ -23,6 +23,9 @@
 "phi" : { 
 "phi" : { "type": "scalar", "desciption": "" }
 }, 
+"shortcut_phi" : { 
+"phi" : { "type": "scalar", "desciption": "" }
+}, 
 "rp" : { 
 "rp.bias" : { "type": "scalar", "desciption": "" }
 "rp.force2" : { "type": "scalar", "desciption": "" }
@@ -44,5 +47,8 @@
 }, 
 "hh" : { 
 "hh" : { "type": "grid", "desciption": "" }
+}, 
+"shortcut_hh" : { 
+"hh" : { "type": "grid", "desciption": "" }
 } 
 } 
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
@@ -806,7 +806,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
           if( as ) {
             unsigned ncomponents = 0; std::vector<ActionWithValue*> val_actions;
             Keywords keys; actionRegister().getKeywords( as->getName(), keys );
-            std::vector<std::string> cnames( keys.getOutputComponents().size() );
+            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();

diff --git a/src/generic/Ones.cpp b/src/generic/Ones.cpp
@@ -45,7 +45,7 @@ PLUMED_REGISTER_ACTION(Ones,"ONES")
 void Ones::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
   keys.add("compulsory","SIZE","the number of ones that you would like to create");
-  keys.setValueDescription("a vector of ones the required number of elements");
+  keys.setValueDescription("a vector of ones with the required number of elements");
   keys.needsAction("CONSTANT");
 }