A faster reconstruction of the request list for the neigborlist

CHANGES/v2.11.md

@@ -5,6 +5,8 @@ This page contains changes that will end up in 2.11
 ### Changes relevant for users:
 
   - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb.
+  - Added the possibility to use the Linked cells algorithm as explained in Allen to build a neighbour list. This can speed up some calculations, when setting up the neigbour list correctly is difficult.
+  - Added the possibility to use the Linked cells algorithm as explained in Allen to the CudaCoordination plugin, removing the upper ceiling on the number of atoms and increasing the performances.
 
 ### Changes relevant for developers:
 

regtest/basic/rt-nl-duplicates-requestlist/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt-nl-duplicates-requestlist/colvar.reference

@@ -0,0 +1,28 @@
+#! FIELDS time c
+ 0.000000   0.0661
+ 1.000000   0.0661
+ 2.000000   0.0661
+ 3.000000   0.0661
+ 4.000000   0.0661
+ 5.000000   0.0661
+ 6.000000   0.0661
+ 7.000000   0.0661
+ 8.000000   0.0661
+ 9.000000   0.0661
+ 10.000000   0.0661
+ 11.000000   0.0661
+ 12.000000   0.0661
+ 13.000000   0.0661
+ 14.000000   0.0661
+ 15.000000   0.0661
+ 16.000000   0.0661
+ 17.000000   0.0661
+ 18.000000   0.0661
+ 19.000000   0.0661
+ 20.000000   0.0661
+ 21.000000   0.0661
+ 22.000000   0.0661
+ 23.000000   0.0661
+ 24.000000   0.0661
+ 25.000000   0.0661
+ 26.000000   0.0661

regtest/basic/rt-nl-duplicates-requestlist/config

@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces ff --dump-forces-fmt=%10.5f --dump-full-virial"