Update NAMD regtests for eABF fix

namd/tests/library/000_dihedralPC_abf2d/namd-version.txt

@@ -1,3 +1,3 @@
-Info: NAMD 2.15alpha2 for Linux-x86_64-multicore
-colvars: Initializing the collective variables module, version 2023-09-05.
-colvars: Using NAMD interface, version "2023-07-06".
+Info: NAMD 3.0b6 for Linux-x86_64-multicore
+colvars: Initializing the collective variables module, version 2024-03-12.
+colvars: Using NAMD interface, version "2023-12-05".

namd/tests/library/018_pathCV/AutoDiff/test.colvars.out

@@ -2,8 +2,11 @@ colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
 colvars:   https://doi.org/10.1080/00268976.2013.813594
 colvars: as well as all other papers listed below for individual features used.
-colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
 colvars: This version was built with the C++11 standard or higher.
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 4)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: available
 colvars: Redefining the Tcl "cv" command to the new script interface.
 colvars: The final output state file will be "test.colvars.state".
 colvars: ----------------------------------------------------------------------
@@ -208,13 +211,14 @@ colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 0 [default]
 colvars:   # timeStepFactor = 1 [default]
 colvars:   # applyBias = on [default]
-colvars:   # updateBias = on [default]
 colvars:   # hideJacobian = off [default]
 colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
 colvars:   # fullSamples = 0
+colvars:   # minSamples = 0 [default]
 colvars:   # inputPrefix =  [default]
 colvars:   # historyFreq = 0 [default]
 colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
 colvars:   # maxForce =  [default]
 colvars:   # CZARestimator = on [default]
 colvars:   # integrate = on [default]
@@ -294,18 +298,20 @@ colvars: updating atomic data (104 atoms).
 colvars: updating group data (0 scalable groups, 0 atoms in total).
 colvars: updating grid object data (0 grid objects in total).
 colvars: updating target temperature (T = 300 K).
+colvars: Current simulation parameters: initial step = 0, integration timestep = 0.5
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "s":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08.
 colvars: Re-initialized atom group for variable "s":1/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08.
 colvars: Re-initialized atom group for variable "z":0/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08.
 colvars: Re-initialized atom group for variable "z":1/0. 104 atoms: total mass = 727.821, total charge = 6.70552e-08.
-colvars: The final output state file will be "test.colvars.state".
 colvars: PathCV WARNING: less than 2 RMSDs are above threshold, selecting 2 closest images
 colvars: PathCV STEP 1   next pathCV flags  1 1
-colvars:   Prepared sample and gradient buffers at step 0.
+colvars:   Initializing extended coordinate to colvar value.
+colvars:   Initializing extended coordinate to colvar value.
 colvars: PathCV WARNING: less than 2 RMSDs are above threshold, selecting 2 closest images
 colvars: PathCV STEP 6   next pathCV flags  1 1
 colvars: PathCV WARNING: less than 2 RMSDs are above threshold, selecting 2 closest images
 colvars: PathCV STEP 11   next pathCV flags  1 1
 colvars: Saving collective variables state to "test.colvars.state".
-colvars:   Integrated in 143 steps, error: 9.02625e-07
-colvars:   Integrated in 142 steps, error: 9.86746e-07
+colvars:   Integrated in 143 steps, error: 8.82141e-07
+colvars:   Integrated in 142 steps, error: 9.86631e-07

namd/tests/library/018_pathCV/AutoDiff/test.colvars.traj

@@ -2,11 +2,11 @@
            0   3.00814883534435e-215 3.00814883534435e-215   5.04223676928709e-01  5.04223676928709e-01  
            1   2.79773744080269e-215 -4.23770774320244e-07   5.04053981240426e-01  5.04219431906761e-01  
            2   2.60900847780748e-215  2.49556789490259e-06   5.04017921282668e-01  5.04210587066118e-01  
-           3   2.48746781445528e-215  1.20892555960855e-05   5.03926056790795e-01  5.04200282559501e-01  
-           4   2.33750613647379e-215  2.56988998248665e-05   5.03744681560205e-01  5.04187067003941e-01  
-           5   2.19483238621295e-215  3.90282685346562e-05   5.03426534412398e-01  5.04174033567399e-01  
-           6   2.06821654791110e-215  5.36535999110737e-05   5.02954037863991e-01  5.04164509109472e-01  
-           7   1.99245194229624e-215  7.03868185877368e-05   5.02333848769048e-01  5.04158701221282e-01  
-           8   1.94607036513624e-215  9.12708950263107e-05   5.01589215390416e-01  5.04154123763789e-01  
-           9   1.90199211917260e-215  1.17295911614485e-04   5.00772663551120e-01  5.04148101532508e-01  
-          10   1.88169145390613e-215  1.40893578825849e-04   4.99983213750952e-01  5.04137015603104e-01  
+           3   2.48746781445528e-215  1.20891510609718e-05   5.03926056790795e-01  5.04200323372613e-01  
+           4   2.33750615487076e-215  2.56986385651233e-05   5.03744681901096e-01  5.04187169006253e-01  
+           5   2.19483246322982e-215  3.90278158394399e-05   5.03426535933299e-01  5.04174210310972e-01  
+           6   2.06821674454760e-215  5.36529298314115e-05   5.02954041985094e-01  5.04164770725786e-01  
+           7   1.99245234508221e-215  7.03859104501844e-05   5.02333857526826e-01  5.04159055782689e-01  
+           8   1.94607108705951e-215  9.12697316901667e-05   5.01589231437258e-01  5.04154577964359e-01  
+           9   1.90199329059870e-215  1.17294478476240e-04   5.00772690129774e-01  5.04148661077250e-01  
+          10   1.88169324270308e-215  1.40891863197231e-04   4.99983254654223e-01  5.04137685451438e-01