Fixed names after Carlo's feedback

all -> allatoms
physical -> mdatoms
virtual removed

See https://github.com/plumed/plumed2/pull/372

CHANGES/v2.5.md

@@ -47,7 +47,7 @@ Changes from version 2.4 which are relevant for users:
   - \ref RMSD calculation has been optimized. This should positively affect the performances of CVs where
      many RMSDs are computed on small groups of atoms, such as secondary structure variables.
   - In \ref METAD, when using a bias factor equal to one (no bias) the `rct` component is set to zero rather than to one.
-  - New shortcuts are available for selecting atoms: `@all`, `@physical`, `@virtual` (see \ref atomSpecs).
+  - New shortcuts are available for selecting atoms: `@allatoms` and `@mdatoms` (see \ref atomSpecs).
   - When using \ref MOLINFO, also the following shortcuts are available for selecting atoms: `@nucleic`, `@protein`, `@water`, `@ions`, `@hydrogens`, `@nonhydrogens`.
   - When using \ref MOLINFO, individual atoms can be chosen also from water molecules (e.g. `@OW-100`).
 

regtest/basic/rt7/plumed.dat

@@ -9,9 +9,10 @@ DUMPATOMS ATOMS=1-108,c1,c2 STRIDE=10 FILE=wrap.xyz
 WRAPAROUND ATOMS=1-108 AROUND=1 GROUPBY=12
 DUMPATOMS ATOMS=1-108 STRIDE=10 FILE=wrap2.xyz
 
-DUMPATOMS ATOMS=@all STRIDE=1 FILE=all.xyz
-DUMPATOMS ATOMS=@physical STRIDE=1 FILE=physical.xyz
-DUMPATOMS ATOMS=@virtual STRIDE=1 FILE=virtual.xyz
+DUMPATOMS ATOMS=@allatoms STRIDE=1 FILE=all.xyz
+DUMPATOMS ATOMS=@mdatoms STRIDE=1 FILE=physical.xyz
+virtuals: GROUP ATOMS=@allatoms REMOVE=@mdatoms
+DUMPATOMS ATOMS=virtuals STRIDE=1 FILE=virtual.xyz
 
 ENDPLUMED
 

src/core/ActionAtomistic.cpp

@@ -175,22 +175,16 @@ void ActionAtomistic::interpretAtomList( std::vector<std::string>& strings, std:
 // here we check if this is a special symbol for MOLINFO
     if( !ok && strings[i].compare(0,1,"@")==0 ) {
       std::string symbol=strings[i].substr(1);
-      if(symbol=="all") {
+      if(symbol=="allatoms") {
         const auto n=plumed.getAtoms().getNatoms() + plumed.getAtoms().getNVirtualAtoms();
         t.reserve(t.size()+n);
         for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
         ok=true;
-      } else if(symbol=="physical") {
+      } else if(symbol=="mdatoms") {
         const auto n=plumed.getAtoms().getNatoms();
         t.reserve(t.size()+n);
         for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
         ok=true;
-      } else if(symbol=="virtual") {
-        const auto n=plumed.getAtoms().getNatoms();
-        const auto v=plumed.getAtoms().getNVirtualAtoms();
-        t.reserve(t.size()+v);
-        for(unsigned i=n; i<n+v; i++) t.push_back(AtomNumber::index(i));
-        ok=true;
       } else {
         vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
         if( moldat.size()>0 ) {

user-doc/Group.md

@@ -15,15 +15,16 @@ predefined as a \subpage GROUP that can be reused multiple times. Lists of atoms
 
 In addition, there are a few shortcuts that can be used:
 
-- `@physical` indicate all the physical atoms present in the MD engine (e.g. `DUMPATOMS ATOMS=@physical`).
-- `@virtual` indicate all the \ref vatoms "virtual atoms" defined within PLUMED (e.g. `DUMPATOMS ATOMS=@virtual`).
-- `@all` indicates all atoms (e.g. `DUMPATOMS ATOMS=@all`).
+- `@mdatoms` indicate all the physical atoms present in the MD engine (e.g. `DUMPATOMS ATOMS=@mdatoms`).
+- `@allatoms` indicates all atoms, including \ref vatoms "those defined only in PLUMED" (e.g. `DUMPATOMS ATOMS=@allatoms`).
+
+The list of the virtual atoms defined in PLUMED can be obtained dy difference with `GROUP ATOMS=@allatoms REMOVE=@mdatoms`.
 
 Other shortcuts are available if you loaded the structure of the molecule using the \ref MOLINFO command.
 
 All the above methods can be combined just putting one name after the other separated by a comma:
 \plumedfile
-DUMPATOMS ATOMS=1,2,10-20,40-60:5,100-70:-2,@virtual LABEL=g5 FILE=test.xyz
+DUMPATOMS ATOMS=1,2,10-20,40-60:5,100-70:-2 LABEL=g5 FILE=test.xyz
 \endplumedfile
 
 Some collective variable must accept a fixed number of atoms, for example a \ref DISTANCE is calculated