Added and run test for reflection for namd

Author: fabsugar

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.out

@@ -1,9 +1,12 @@
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
-colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
+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 (num threads = 4).
 colvars: This version was built with the C++11 standard or higher.
+colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars: The final output state file will be "test.colvars.state".
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -42,54 +45,55 @@ colvars: # colvarsTrajFrequency = 1
 colvars: # colvarsRestartFrequency = 10
 colvars: # scriptedColvarForces = off [default]
 colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
 colvars:   # name = "one"
 colvars:   Initializing a new "distance" component.
+colvars:   # name = "" [default]
+colvars:   # componentCoeff = 1 [default]
+colvars:   # componentExp = 1 [default]
+colvars:   # period = 0 [default]
+colvars:   # wrapAround = 0 [default]
+colvars:   # forceNoPBC = off [default]
+colvars:   # scalable = on [default]
+colvars:     Initializing atom group "group1".
 colvars:     # name = "" [default]
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # scalable = on [default]
-colvars:       Initializing atom group "group1".
-colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
-colvars:       # atomsOfGroup = "" [default]
-colvars:       # indexGroup = "group1"
-colvars:       # psfSegID =  [default]
-colvars:       # atomsFile = "" [default]
-colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
-colvars:       # enableFitGradients = on [default]
-colvars:       Enabling scalable calculation for group "group1".
-colvars:       # printAtomIDs = off [default]
-colvars:       Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72.
-colvars:       Initializing atom group "group2".
-colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
-colvars:       # atomsOfGroup = "" [default]
-colvars:       # indexGroup = "group2"
-colvars:       # psfSegID =  [default]
-colvars:       # atomsFile = "" [default]
-colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
-colvars:       # enableFitGradients = on [default]
-colvars:       Enabling scalable calculation for group "group2".
-colvars:       # printAtomIDs = off [default]
-colvars:       Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4.
-colvars:     # oneSiteSystemForce = off [default]
-colvars:     # oneSiteTotalForce = off [default]
+colvars:     # centerToOrigin = off [default]
+colvars:     # centerToReference = off [default]
+colvars:     # rotateToReference = off [default]
+colvars:     # atomsOfGroup = "" [default]
+colvars:     # indexGroup = "group1"
+colvars:     # psfSegID =  [default]
+colvars:     # atomsFile = "" [default]
+colvars:     # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:     # enableFitGradients = on [default]
+colvars:     Enabling scalable calculation for group "group1".
+colvars:     # printAtomIDs = off [default]
+colvars:     Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72.
+colvars:     Initializing atom group "group2".
+colvars:     # name = "" [default]
+colvars:     # centerToOrigin = off [default]
+colvars:     # centerToReference = off [default]
+colvars:     # rotateToReference = off [default]
+colvars:     # atomsOfGroup = "" [default]
+colvars:     # indexGroup = "group2"
+colvars:     # psfSegID =  [default]
+colvars:     # atomsFile = "" [default]
+colvars:     # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:     # enableFitGradients = on [default]
+colvars:     Enabling scalable calculation for group "group2".
+colvars:     # printAtomIDs = off [default]
+colvars:     Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4.
+colvars:   # oneSiteSystemForce = off [default]
+colvars:   # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
 colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 0.5
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # upperBoundary = 10
-colvars:   # hardLowerBoundary = on [default]
-colvars:   # hardUpperBoundary = off [default]
+colvars:   # lowerBoundary = 3.2
+colvars:   # upperBoundary = 10.2
+colvars:   # hardLowerBoundary = on
+colvars:   # hardUpperBoundary = on
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
@@ -102,6 +106,25 @@ colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "harmonicwalls" instance.
+colvars:   # name = "wall_one"
+colvars:   # colvars = { one }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # forceConstant = 1
+colvars:   # decoupling = off [default]
+colvars:   # targetForceConstant = -1 [default]
+colvars:   # lowerWalls = { 3.2 }
+colvars:   # upperWalls = { 10.2 }
+colvars:   # lowerWallConstant = 1 [default]
+colvars:   # upperWallConstant = 1 [default]
+colvars:   The lower wall force constant for colvar "one" will be rescaled to 4 according to the specified width (0.5).
+colvars:   The upper wall force constant for colvar "one" will be rescaled to 4 according to the specified width (0.5).
+colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "metadynamics" instance.
 colvars:   # name = "metadynamics1" [default]
 colvars:   # colvars = { one }
@@ -127,28 +150,55 @@ colvars:   # keepFreeEnergyFiles = off [default]
 colvars:   # writeHillsTrajectory = off [default]
 colvars:   # wellTempered = off [default]
 colvars:   # biasTemperature = -1 [default]
+colvars:   # useHillsReflection = on
+colvars:   # reflectionRange = 6 [default]
+colvars:   Reflection range is 6.
+colvars:   # reflectionLowLimitUseCVs =  [default]
+colvars:   Using all non-periodic variables for lower limits of reflection 
+colvars:   # reflectionUpLimitUseCVs =  [default]
+colvars:   Using all non-periodic variables for upper limits of reflection 
+colvars:   # reflectionLowLimit = { 3.2 } [default]
+colvars:   Reflection condition is applied on a lower limit for CV 0.
+colvars:   Reflection condition lower limit for this CV is 3.2.
+colvars:   # reflectionUpLimit = { 10.2 } [default]
+colvars:   Reflection condition is applied on an upper limit for CV 0.
+colvars:   Reflection condition upper limit for this CV is 10.2.
 colvars:   # ebMeta = off [default]
 colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
+colvars: Collective variables biases initialized, 2 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
 colvars: Updating NAMD interface:
 colvars: updating atomic data (0 atoms).
 colvars: updating group data (2 scalable groups, 8 atoms in total).
-colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
-colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
-colvars: The restart output state file will be "test.tmp.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
-colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars: - Metadynamics colvar bias implementation:
+colvars: - Optimal rotation via flexible fitting:
+colvars: - distance colvar component:
+colvars: - harmonicWalls colvar bias implementation:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - NAMD engine:
+colvars: - Scalable center-of-mass computation (NAMD):
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 0 K).
 colvars: Updating NAMD interface:
 colvars: updating atomic data (0 atoms).
 colvars: updating group data (2 scalable groups, 8 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: updating target temperature (T = 0 K).
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
 colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: The restart output state file will be "test.tmp.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Saving collective variables state to "test.tmp.colvars.state".

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.state.stripped

@@ -5,40 +5,45 @@ configuration {
 
 colvar {
   name one
-  x  3.21688278597333e+00
+  x       3.2168853380692
+}
+
+restraint {
+  configuration {
+step 20
+name wall_one
+  }
 }
 
 metadynamics {
   configuration {
-    step 20
-    name metadynamics1
+step 20
+name metadynamics1
   }
-  hills_energy
+
+hills_energy
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
-  sizes  20
+  lower_boundaries  3.2
+  upper_boundaries  10.2
+  widths  0.5
+  sizes  14
 }
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04
- 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-06
+ 2.90793197471122e-03 2.29589040998682e-04 1.43098718458920e-06
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00
-  hills_energy_gradients
+
+hills_energy_gradients
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
-  sizes  20
+  lower_boundaries  3.2
+  upper_boundaries  10.2
+  widths  0.5
+  sizes  14
 }
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03
- -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-05
+ -7.38291182480299e-03 -1.74872845262777e-03 -1.81663860935017e-05
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.traj

@@ -1,22 +1,22 @@
-# step         one                   fa_one                
-           0    3.20554673468334e+00  0.00000000000000e+00 
-           1    3.20437148316546e+00  0.00000000000000e+00 
-           2    3.20384028589204e+00  0.00000000000000e+00 
-           3    3.20396721187433e+00  0.00000000000000e+00 
-           4    3.20472817287036e+00  0.00000000000000e+00 
-           5    3.20606308066645e+00  0.00000000000000e+00 
-           6    3.20787989003051e+00  0.00000000000000e+00 
-           7    3.21005997943917e+00  0.00000000000000e+00 
-           8    3.21246460655188e+00  0.00000000000000e+00 
-           9    3.21494247388772e+00  0.00000000000000e+00 
-          10    3.21733851236362e+00  3.30884583259955e-04 
-          11    3.21950367891521e+00  3.30884583259955e-04 
-          12    3.22130501376020e+00  3.30884583259955e-04 
-          13    3.22263482513293e+00  3.30884583259955e-04 
-          14    3.22341774651982e+00  3.30884583259955e-04 
-          15    3.22361481079113e+00  3.30884583259955e-04 
-          16    3.22322427751010e+00  3.30884583259955e-04 
-          17    3.22227956023865e+00  3.30884583259955e-04 
-          18    3.22084496840419e+00  3.30884583259955e-04 
-          19    3.21901000786075e+00  3.30884583259955e-04 
-          20    3.21688278597333e+00  6.66334787942696e-04 
+# step         one                   fa_one                 
+           0    3.20554673468334e+00  0.00000000000000e+00  
+           1    3.20437148316484e+00  0.00000000000000e+00  
+           2    3.20384028588952e+00  0.00000000000000e+00  
+           3    3.20396721186862e+00  0.00000000000000e+00  
+           4    3.20472817286016e+00  0.00000000000000e+00  
+           5    3.20606308065050e+00  0.00000000000000e+00  
+           6    3.20787989000757e+00  0.00000000000000e+00  
+           7    3.21005997940810e+00  0.00000000000000e+00  
+           8    3.21246460651160e+00  0.00000000000000e+00  
+           9    3.21494247383722e+00  0.00000000000000e+00  
+          10    3.21733851230199e+00  3.69111079117202e-03  
+          11    3.21950373044117e+00  3.69111079117202e-03  
+          12    3.22130516783262e+00  3.69111079117202e-03  
+          13    3.22263513141286e+00  3.69111079117202e-03  
+          14    3.22341825276891e+00  3.69111079117202e-03  
+          15    3.22361556235479e+00  3.69111079117202e-03  
+          16    3.22322531690825e+00  3.69111079117202e-03  
+          17    3.22228092687886e+00  3.69111079117202e-03  
+          18    3.22084669842434e+00  3.69111079117202e-03  
+          19    3.21901213410055e+00  3.69111079117202e-03  
+          20    3.21688533806922e+00  7.38291182480299e-03  

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.pmf

@@ -1,23 +1,17 @@
 # 1
-#  0.00000000000000e+00  5.00000000000000e-01         20  0
+#  3.20000000000000e+00  5.00000000000000e-01         14  0
 
-  2.50000000000000e-01   1.98901157291202e-03
-  7.50000000000000e-01   1.98901157291202e-03
-  1.25000000000000e+00   1.98901157291202e-03
-  1.75000000000000e+00   1.98897688086274e-03
-  2.25000000000000e+00   1.97193947190077e-03
-  2.75000000000000e+00   1.33071323762382e-03
-  3.25000000000000e+00  -0.00000000000000e+00
-  3.75000000000000e+00   1.51810946847522e-03
-  4.25000000000000e+00   1.98027577214821e-03
-  4.75000000000000e+00   1.98901157291202e-03
-  5.25000000000000e+00   1.98901157291202e-03
-  5.75000000000000e+00   1.98901157291202e-03
-  6.25000000000000e+00   1.98901157291202e-03
-  6.75000000000000e+00   1.98901157291202e-03
-  7.25000000000000e+00   1.98901157291202e-03
-  7.75000000000000e+00   1.98901157291202e-03
-  8.25000000000000e+00   1.98901157291202e-03
-  8.75000000000000e+00   1.98901157291202e-03
-  9.25000000000000e+00   1.98901157291202e-03
-  9.75000000000000e+00   1.98901157291202e-03
+  3.45000000000000e+00  -0.00000000000000e+00
+  3.95000000000000e+00   2.67834293371254e-03
+  4.45000000000000e+00   2.90650098752663e-03
+  4.95000000000000e+00   2.90793197471122e-03
+  5.45000000000000e+00   2.90793197471122e-03
+  5.95000000000000e+00   2.90793197471122e-03
+  6.45000000000000e+00   2.90793197471122e-03
+  6.95000000000000e+00   2.90793197471122e-03
+  7.45000000000000e+00   2.90793197471122e-03
+  7.95000000000000e+00   2.90793197471122e-03
+  8.45000000000000e+00   2.90793197471122e-03
+  8.95000000000000e+00   2.90793197471122e-03
+  9.45000000000000e+00   2.90793197471122e-03
+  9.95000000000000e+00   2.90793197471122e-03