From 9100551cb6dcdb19f56a49a09fb35aa5be1845de Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 6 Feb 2025 15:29:21 +0100
Subject: [PATCH] Removed creation of vatoms when using DISTANCES GROUPA/GROUPB
 syntax (#1193)

* Removed creation of vatoms when using DISTANCES GROUPA/GROUPB syntax

* Added details of changes made yesterday to change log

---------

Co-authored-by: Gareth Aneurin Tribello <garethtribello@dhcp-129-242.wifi.sissa.it>
---
 CHANGES/v2.10.md              |  1 +
 src/multicolvar/Distances.cpp | 19 -------------------
 2 files changed, 1 insertion(+), 19 deletions(-)

diff --git a/CHANGES/v2.10.md b/CHANGES/v2.10.md
index 1282e5b776..446793e87f 100644
--- a/CHANGES/v2.10.md
+++ b/CHANGES/v2.10.md
@@ -41,6 +41,7 @@ Before switching to version 2.10, users are invited to carefully read the follow
   - Action NBONDS no longer exists.  The same effect can be achieved through a more transparent implementation that you can read about here: https://plumed-school.github.io/lessons/23/001/data/Steinhardt.html
   - Action CENTER_OF_MULTICOLVAR no longer exists.  You now simply use \ref CENTER with the PHASES option and a vector as input for the weights.
   - Dimensionality reduction methods and landmark selection actions have a new syntax. A good introduction that explains how to use these actions can be found in [this tutorial](https://plumed-school.github.io/lessons/21/006/data/DIMENSIONALITY.html)
+  - if you use \ref DISTANCES with the GROUP or GROUPA/GROUPB syntax each distance is no longer allocated to a position in space.  You thus cannot use the GROUP or GROUPA/GROUPB variants of action with methods such as \ref DUMPMULTICOLVAR, \ref MULTICOLVARDENS or \ref SMAC.  To be clear if you use \DISTANCES with the ATOMS1/ATOMS2/ATOMS3/... syntax you can still use it with \ref DUMPMULTICOLVAR, \ref MULTICOLVARDENS or \ref SMAC.  We believe this second use case was the variant of the old version that was widely used.
 
 - Places where we strongly recommend using the new sytax:
   - If you are using \ref DFSCLUSTERING and the \ref CLUSTER_PROPERTIES or \ref CLUSTER_DISTRIBUTION actions you are strongly encouraged to read: https://plumed-school.github.io/lessons/23/001/data/Clusters.html
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index 09c797304f..89f9a4ff76 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -279,32 +279,13 @@ Distances::Distances(const ActionOptions& ao):
       if( grpb.size()==0 ) {
         error("found GROUPA but no corresponding GROUPB");
       }
-      std::string grpstr = getShortcutLabel() + "_grp: GROUP ATOMS=";
       bool printcomment=false;
       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];
-          if( i*grpb.size() + j<6 ) {
-            readInputLine( getShortcutLabel() + "_vatom" + num + ": CENTER ATOMS=" + grpa[i] + "," + grpb[j], true );
-          } else {
-            readInputLine( getShortcutLabel() + "_vatom" + num + ": CENTER ATOMS=" + grpa[i] + "," + grpb[j], false );
-            printcomment=true;
-          }
-          if( i+j==0 ) {
-            grpstr += getShortcutLabel() + "_vatom" + num;
-          } else {
-            grpstr += "," + getShortcutLabel() + "_vatom" + num;
-          }
         }
       }
-      std::string num;
-      Tools::convert( grpa.size()*grpb.size(), num );
-      if( printcomment ) {
-        addCommentToShortcutOutput("# A further " + num + " CENTER like the ones above were also created but are not shown");
-      }
-      readInputLine( grpstr );
     } else {
       std::string grpstr = getShortcutLabel() + "_grp: GROUP ATOMS=";
       for(unsigned i=1;; ++i) {