From c49e339318f1b660ac8a4cb2d5e1f6cb01c97686 Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Mon, 20 Jan 2025 14:57:04 +0000
Subject: [PATCH 1/3] Added code to link cell to ensure all atoms are put in a
 single link cell if there are no pbcs

---
 src/tools/LinkCells.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/tools/LinkCells.cpp b/src/tools/LinkCells.cpp
index 603cfe7849..ab55875b2f 100644
--- a/src/tools/LinkCells.cpp
+++ b/src/tools/LinkCells.cpp
@@ -47,13 +47,15 @@ void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vecto
   plumed_assert( cutoffwasset && pos.size()==indices.size() );
 
   // Must be able to check that pbcs are not nonsensical in some way?? -- GAT
-
-  double determinant = pbc.getBox().determinant();
-
-  plumed_assert(determinant > epsilon) <<"Cell lists cannot be built when passing a box with null volume. Volume is "<<determinant;
-
+  auto box = pbc.getBox();
+  if(box(0,0)==0.0 && box(0,1)==0.0 && box(0,2)==0.0 && box(1,0)==0.0 && box(1,1)==0.0 && box(1,2)==0.0 && box(2,0)==0.0 && box(2,1)==0 && box(2,2)==0) {
+    box(0,0) = box(1,1) = box(2,2) = 1e200;
+  } else {
+    auto determinant = box.determinant();
+    plumed_assert(determinant > epsilon) <<"Cell lists cannot be built when passing a box with null volume. Volume is "<<determinant;
+  }
   // Setup the pbc object by copying it from action
-  mypbc.setBox( pbc.getBox() );
+  mypbc.setBox( box );
 
   // Setup the lists
   if( pos.size()!=allcells.size() ) {
@@ -91,9 +93,7 @@ void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vecto
     lcell_starts.resize( ncellstot );
   }
   // Clear nlcells
-  for(unsigned i=0; i<ncellstot; ++i) {
-    lcell_tots[i]=0;
-  }
+  lcell_tots.assign( lcell_tots.size(), 0 );
   // Clear allcells
   allcells.assign( allcells.size(), 0 );
 

From 63369114d7b130fd8b4ce44fd3423e23f96d78bc Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Mon, 20 Jan 2025 15:54:08 +0000
Subject: [PATCH 2/3] Second attempt to ensure all atoms are in single link
 cell if structure has nopbc

---
 src/tools/LinkCells.cpp | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/tools/LinkCells.cpp b/src/tools/LinkCells.cpp
index ab55875b2f..e1851e5d93 100644
--- a/src/tools/LinkCells.cpp
+++ b/src/tools/LinkCells.cpp
@@ -49,7 +49,7 @@ void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vecto
   // Must be able to check that pbcs are not nonsensical in some way?? -- GAT
   auto box = pbc.getBox();
   if(box(0,0)==0.0 && box(0,1)==0.0 && box(0,2)==0.0 && box(1,0)==0.0 && box(1,1)==0.0 && box(1,2)==0.0 && box(2,0)==0.0 && box(2,1)==0 && box(2,2)==0) {
-    box(0,0) = box(1,1) = box(2,2) = 1e200;
+    box(0,0) = box(1,1) = box(2,2) = link_cutoff;
   } else {
     auto determinant = box.determinant();
     plumed_assert(determinant > epsilon) <<"Cell lists cannot be built when passing a box with null volume. Volume is "<<determinant;
@@ -114,7 +114,7 @@ void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vecto
     tot+=lcell_tots[i];
     lcell_tots[i]=0;
   }
-  plumed_assert( tot==pos.size() );
+  plumed_assert( tot==pos.size() ) <<"Total number of atoms found in link cells is "<<tot<<" number of atoms is "<<pos.size();
 
   // And setup the link cells properly
   for(unsigned j=0; j<pos.size(); ++j) {
@@ -186,8 +186,12 @@ void LinkCells::retrieveAtomsInCells( const unsigned& ncells_required,
 }
 
 std::array<unsigned,3> LinkCells::findMyCell( const Vector& pos ) const {
-  Vector fpos=mypbc.realToScaled( pos );
   std::array<unsigned,3> celn;
+  if( ncells[0]*ncells[1]*ncells[2] == 1 ) {
+    celn[0]=celn[1]=celn[2]=0;
+    return celn;
+  }
+  Vector fpos=mypbc.realToScaled( pos );
   for(unsigned j=0; j<3; ++j) {
     celn[j] = std::floor( ( Tools::pbc(fpos[j]) + 0.5 ) * ncells[j] );
     plumed_assert( celn[j]>=0 && celn[j]<ncells[j] ); // Check that atom is in box

From 6def33f5a1d86d36b5d25d97c4bbc803161ed432 Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@gareths-mbp.mp.qub.ac.uk>
Date: Wed, 22 Jan 2025 09:37:57 +0000
Subject: [PATCH 3/3] Hopefully fixes issue with link cells when pbc are not
 set.

---
 src/tools/LinkCells.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/tools/LinkCells.cpp b/src/tools/LinkCells.cpp
index e1851e5d93..6cd19bc09f 100644
--- a/src/tools/LinkCells.cpp
+++ b/src/tools/LinkCells.cpp
@@ -49,7 +49,10 @@ void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vecto
   // Must be able to check that pbcs are not nonsensical in some way?? -- GAT
   auto box = pbc.getBox();
   if(box(0,0)==0.0 && box(0,1)==0.0 && box(0,2)==0.0 && box(1,0)==0.0 && box(1,1)==0.0 && box(1,2)==0.0 && box(2,0)==0.0 && box(2,1)==0 && box(2,2)==0) {
-    box(0,0) = box(1,1) = box(2,2) = link_cutoff;
+    // If the box is not set then we can't use link cells.  We thus set the link cell cutoff and box vectors equal to 23 (because it is the best number).
+    // Setting everything this way ensures that the link cells are a 1x1x1 box.  Notice that if it is a one by one by one box then we are hard coded to return
+    // 0 in findCell
+    box(0,0) = box(1,1) = box(2,2) = link_cutoff = 23;
   } else {
     auto determinant = box.determinant();
     plumed_assert(determinant > epsilon) <<"Cell lists cannot be built when passing a box with null volume. Volume is "<<determinant;