Fixes to documentation generators for PlumedToHTML (#1081)

* Rewritten code for getting the descriptions of values so that we get keywords in a way that will work with LOAD * Modified the way the documentation is got when you output the value dictionary in driver so that you can use action labels that have dots in them Also added a warning to try to stop people from using dots in the labels for actions as it is not a great idea * Changed names of actions created by the XAngles shortcut to ensure that an input on the nest continues working * Fixed final problems with building nest inputs and ran astyle --------- Co-authored-by: Gareth Aneurin Tribello <garethtribello@gareths-mbp.mp.qub.ac.uk>
plumed · May 22, 2024 · f9b0bd9 · f9b0bd9 · PlumedBot · May 22, 2024
1 parent 2434e5c
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Showing 8 changed files with 34 additions and 18 deletions.
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
@@ -27,7 +27,6 @@
 #include "core/ActionWithValue.h"
 #include "core/ActionWithVirtualAtom.h"
 #include "core/ActionShortcut.h"
-#include "core/ActionRegister.h"
 #include "tools/Communicator.h"
 #include "tools/Random.h"
 #include "tools/Pbc.h"
@@ -788,14 +787,17 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
           }
           ActionWithValue* av=dynamic_cast<ActionWithValue*>(pp.get());
           if( av && av->getNumberOfComponents()>0 ) {
-            Keywords keys; actionRegister().getKeywords( av->getName(), keys );
+            Keywords keys; p.getKeywordsForAction( av->getName(), keys );
             if( firsta ) { valuefile.printf("  \"%s\" : {\n    \"action\" : \"%s\"", av->getLabel().c_str(), keys.getDisplayName().c_str() ); firsta=false; }
             else valuefile.printf(",\n  \"%s\" : {\n    \"action\" : \"%s\"", av->getLabel().c_str(), keys.getDisplayName().c_str() );
             for(unsigned i=0; i<av->getNumberOfComponents(); ++i) {
-              Value* myval = av->copyOutput(i); 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 = av->getOutputComponentDescription( cname, keys );
-              } else description = keys.getOutputComponentDescription(".#!value");
+              Value* myval = av->copyOutput(i); std::string compname = myval->getName(), description;
+              if( av->getLabel()==compname ) {
+                description = keys.getOutputComponentDescription(".#!value");
+              } else {
+                std::size_t dot=compname.find(av->getLabel() + "."); std::string cname = compname.substr(dot + av->getLabel().length() + 1);
+                description = av->getOutputComponentDescription( cname, keys );
+              }
               if( description.find("\\")!=std::string::npos ) error("found invalid backslash character in documentation for component " + compname + " in action " + av->getName() + " with label " + av->getLabel() );
               valuefile.printf(",\n    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() );
             }
@@ -808,7 +810,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
 
             if( firsta ) { valuefile.printf("  \"shortcut_%s\" : {\n    \"action\" : \"%s\"", as->getShortcutLabel().c_str(), as->getName().c_str() ); firsta=false; }
             else valuefile.printf(",\n  \"shortcut_%s\" : {\n    \"action\" : \"%s\"", as->getShortcutLabel().c_str(), as->getName().c_str() );
-            Keywords keys; actionRegister().getKeywords( as->getName(), keys );
+            Keywords keys; p.getKeywordsForAction( 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] );
@@ -820,10 +822,13 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
                 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");
+                  Value* myval = av2->copyOutput(j); std::string compname = myval->getName(), description;
+                  if( av2->getLabel()==compname ) {
+                    plumed_merror("should not be outputting description of value from action when using shortcuts");
+                  } else {
+                    std::size_t dot=compname.find(av2->getLabel() + "."); std::string cname = compname.substr(dot+av2->getLabel().length() + 1);
+                    description = av2->getOutputComponentDescription( cname, keys );
+                  }
                   if( description.find("\\")!=std::string::npos ) error("found invalid backslash character in documentation for component " + compname + " in action " + av2->getName() + " with label " + av2->getLabel() );
                   valuefile.printf(",\n    \"%s\" : { \"type\": \"%s\", \"description\": \"%s\" }", myval->getName().c_str(), myval->getValueType().c_str(), description.c_str() );
                 }

diff --git a/src/core/Action.cpp b/src/core/Action.cpp
@@ -97,7 +97,7 @@ Action::Action(const ActionOptions&ao):
   if(label.length()==0) {
     std::string s; Tools::convert(plumed.getActionSet().size()-plumed.getActionSet().select<ActionForInterface*>().size(),s);
     label="@"+s;
-  }
+  } else if ( label.find(".")!=std::string::npos ) warning("using full stop in an action label should be avaoided as . has a special meaning in PLUMED action labels");
   if( plumed.getActionSet().selectWithLabel<Action*>(label) ) error("label " + label + " has been already used");
   if( !keywords.exists("NO_ACTION_LOG") ) log.printf("  with label %s\n",label.c_str());
   if ( keywords.exists("UPDATE_FROM") ) parse("UPDATE_FROM",update_from);

diff --git a/src/core/ActionRegister.cpp b/src/core/ActionRegister.cpp
@@ -93,4 +93,8 @@ bool ActionRegister::getKeywords(const std::string& action, Keywords& keys) {
   return false;
 }
 
+void ActionRegister::getKeywords(const std::vector<void*> & images, const std::string& action, Keywords& keys) {
+  auto content=get(images,action); keys.thisactname = action; content.keys(keys);
+}
+
 }
diff --git a/src/core/ActionRegister.h b/src/core/ActionRegister.h
@@ -64,6 +64,7 @@ class ActionRegister:
   bool printManual(const std::string& action, const bool& vimout, const bool& spellout);
 /// Retrieve a keywords object for a particular action
   bool getKeywords( const std::string& action, Keywords& keys );
+  void getKeywords(const std::vector<void*> & images, const std::string& action, Keywords& keys);
 /// Print out a template command for an action
   bool printTemplate(const std::string& action, bool include_optional);
   std::vector<std::string> getActionNames() const;

diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
@@ -170,7 +170,6 @@ void ActionWithValue::addComponentWithDerivatives( const std::string& name, cons
 
 std::string ActionWithValue::getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const {
   std::size_t und=cname.find_last_of("_"); std::size_t hyph=cname.find_first_of("-");
-  if( und!=std::string::npos && hyph!=std::string::npos ) plumed_merror("cannot use underscore and hyphen in name");
   if( und!=std::string::npos ) return keys.getOutputComponentDescription(cname.substr(und)) + " This particular component measures this quantity for the input CV named " + cname.substr(0,und);
   if( hyph!=std::string::npos ) return keys.getOutputComponentDescription(cname.substr(0,hyph)) + "  This is the " + cname.substr(hyph+1) + "th of these quantities";
   plumed_massert( keys.outputComponentExists(cname), "component " + cname + " does not exist in " + keys.getDisplayName() + " if the component names are customizable then you should override this function" );

diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
@@ -1488,6 +1488,10 @@ bool PlumedMain::parseOnlyMode() const {
   return doParseOnly;
 }
 
+void PlumedMain::getKeywordsForAction( const std::string& action, Keywords& keys ) const {
+  actionRegister().getKeywords( dlloader.getHandles(), action, keys );
+}
+
 #ifdef __PLUMED_HAS_PYTHON
 // This is here to stop cppcheck throwing an error
 #endif

diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
@@ -68,6 +68,7 @@ class FileBase;
 class TypesafePtr;
 class IFile;
 class Units;
+class Keywords;
 class DataPassingTools;
 
 /**
@@ -523,6 +524,8 @@ class PlumedMain:
   void plumedQuantityToMD( const std::string& unit, const double& eng, const TypesafePtr & m) const ;
 /// Take a typesafe pointer from the MD code and convert it to a double
   double MDQuantityToPLUMED( const std::string& unit, const TypesafePtr & m) const ;
+/// Get the keywords for a particular action
+  void getKeywordsForAction( const std::string& action, Keywords& keys ) const ;
 };
 
 /////

diff --git a/src/multicolvar/XAngle.cpp b/src/multicolvar/XAngle.cpp
@@ -76,7 +76,7 @@ XAngle::XAngle(const ActionOptions& ao):
   ActionShortcut(ao)
 {
   // Create distances
-  std::string dline = getShortcutLabel() + ": DISTANCE COMPONENTS";
+  std::string dline = getShortcutLabel() + "_dists: DISTANCE COMPONENTS";
   for(unsigned i=1;; ++i) {
     std::string atstring; parseNumbered("ATOMS",i,atstring);
     if( atstring.length()==0 ) break;
@@ -85,11 +85,11 @@ XAngle::XAngle(const ActionOptions& ao):
   }
   readInputLine( dline );
   // Normalize the vectors
-  readInputLine( getShortcutLabel() + "_norm2: COMBINE ARG=" + getShortcutLabel() + ".x" + "," + getShortcutLabel() + ".y," + getShortcutLabel() + ".z POWERS=2,2,2 PERIODIC=NO");
+  readInputLine( getShortcutLabel() + "_norm2: COMBINE ARG=" + getShortcutLabel() + "_dists.x" + "," + getShortcutLabel() + "_dists.y," + getShortcutLabel() + "_dists.z POWERS=2,2,2 PERIODIC=NO");
   readInputLine( getShortcutLabel() + "_norm: CUSTOM ARG=" + getShortcutLabel() + "_norm2 FUNC=sqrt(x) PERIODIC=NO");
-  readInputLine( getShortcutLabel() + "_norm_x: CUSTOM ARG=" + getShortcutLabel() + ".x," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
-  readInputLine( getShortcutLabel() + "_norm_y: CUSTOM ARG=" + getShortcutLabel() + ".y," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
-  readInputLine( getShortcutLabel() + "_norm_z: CUSTOM ARG=" + getShortcutLabel() + ".z," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
+  readInputLine( getShortcutLabel() + "_norm_x: CUSTOM ARG=" + getShortcutLabel() + "_dists.x," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
+  readInputLine( getShortcutLabel() + "_norm_y: CUSTOM ARG=" + getShortcutLabel() + "_dists.y," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
+  readInputLine( getShortcutLabel() + "_norm_z: CUSTOM ARG=" + getShortcutLabel() + "_dists.z," + getShortcutLabel() + "_norm FUNC=x/y PERIODIC=NO");
   // Now compute the angles with matheval
   if( getName()=="XANGLES" ) readInputLine( getShortcutLabel() + "_ang: CUSTOM FUNC=acos(x) PERIODIC=NO ARG=" + getShortcutLabel() + "_norm_x");
   if( getName()=="YANGLES" ) readInputLine( getShortcutLabel() + "_ang: CUSTOM FUNC=acos(x) PERIODIC=NO ARG=" + getShortcutLabel() + "_norm_y");