More features from hack-the-tree (#1033)

* Got rid of MultiRMSD action as it makes no sense and now doing DRMSD using a shortcut * RMSD no longer depends on reference class * Started adding shortcut for RMSD action * Rewritten PCAVARS as a shortcut that uses multiple actions and shows how this is matrix vector multiplication * Reimplemented PATH and GPROPERTYMAP using features of new code * Simplification of RMSD vector and PCAVARS * Added new version of geometric path that is computed via trigonometry * Added new version of pathtools that doesn't rely on reference class * Fixed adaptive path to work with new style distances * Removed code that is no longer used * Added DRMSD metric for PATHs * Ran astyle and fixed json file * Fixed a number of issues that were flagged by ccpcheck * Added requirement to these regtests so they are not run when modules required are not compiled * Got rid of an exception in VSTACK as it is overly specific * Fixed bug that occurs try to convert a PDB with no atoms to a constant * Fixed out of bounds error when applying GeometricPath * Small fixes for things flagged up by code review by Github tools and Giovanni --------- Co-authored-by: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local> Co-authored-by: Gareth Aneurin Tribello <garethtribello@gareths-mbp.mp.qub.ac.uk>
plumed · Mar 6, 2024 · 6a56f54 · 6a56f54 · PlumedBot · Mar 6, 2024
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diff --git a/regtest/adjmat/rt-graph-2/graph.md.reference b/regtest/adjmat/rt-graph-2/graph.md.reference
@@ -32,9 +32,6 @@ subgraph subc1 [c1]
 end
 cc -- ones --> ones
 linkStyle 6 stroke:blue,color:blue;
-ones(["label=ones 
- CONSTANT 
-"])
 Box("label=Box 
  PBC 
 ")

diff --git a/regtest/adjmat/rt-graph-4/graph.md.reference b/regtest/adjmat/rt-graph-4/graph.md.reference
@@ -78,9 +78,6 @@ subgraph subcm_cncn [cm_cncn]
 end
 cc_cnI -- ones192 --> ones192
 linkStyle 17 stroke:blue,color:blue;
-ones192(["label=ones192 
- CONSTANT 
-"])
 subgraph subcm_cncn [cm_cncn]
 end
 cc_cnpb -- ones64 --> ones64
@@ -89,9 +86,6 @@ subgraph subcm_cncn [cm_cncn]
 end
 cc_cncn -- ones64 --> ones64
 linkStyle 19 stroke:blue,color:blue;
-ones64(["label=ones64 
- CONSTANT 
-"])
 Box("label=Box 
  PBC 
 ")

diff --git a/regtest/basic/rt-drmsd/config b/regtest/basic/rt-drmsd/config
@@ -1,3 +1,4 @@
+plumed_modules=adjmat
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"

diff --git a/regtest/basic/rt-molfile-1/COLVAR.reference b/regtest/basic/rt-molfile-1/COLVAR.reference
@@ -1,4 +1,4 @@
-#! FIELDS time rmsd0 rmsd1 sum @4.bias @4.force2
+#! FIELDS time rmsd0 rmsd1 sum @6.bias @6.force2
  0.000000  0.000  0.149  0.149 197.034 394.068
  0.005000  0.072  0.160  0.231 195.399 390.797
  0.010000  0.032  0.147  0.178 196.450 392.899

diff --git a/regtest/basic/rt-molfile-2/COLVAR.reference b/regtest/basic/rt-molfile-2/COLVAR.reference
@@ -1,4 +1,4 @@
-#! FIELDS time rmsd0 rmsd1 sum @4.bias @4.force2
+#! FIELDS time rmsd0 rmsd1 sum @6.bias @6.force2
  0.000000  0.000  0.149  0.149 197.034 394.068
  0.005000  0.072  0.160  0.231 195.399 390.797
  0.010000  0.032  0.147  0.178 196.450 392.899

diff --git a/regtest/basic/rt-multirmsd/config b/regtest/basic/rt-multirmsd/config
@@ -1,3 +1,4 @@
+plumed_modules=adjmat
 type=driver
 # this is to test a different name
 arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"

diff --git a/regtest/basic/rt-multirmsd/deriv.reference b/regtest/basic/rt-multirmsd/deriv.reference