Regtest for lambda-ABF in NAMD

namd/src/colvarproxy_namd.C

@@ -1656,7 +1656,7 @@ int colvarproxy_namd::request_alch_energy_freq(int const freq) {
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchOn) {
-    cvm::error("alch must be enabled for lambda-dynamics.\n");
+    cvm::error("alchOn must be enabled for lambda-dynamics.\n");
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchThermIntOn) {

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out

@@ -0,0 +1,120 @@
+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: 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 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]
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 10 [default]
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "lambda"
+colvars:   Initializing a new "alchLambda" component.
+colvars:   Warning: cannot cite unknown feature "alchLambda colvar 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:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0
+colvars:   # upperBoundary = 1
+colvars:   # hardLowerBoundary = off [default]
+colvars:   # hardUpperBoundary = off [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = on
+colvars:     Enabling the extended Lagrangian term for colvar "lambda".
+colvars:     # extendedTemp = 300 [default]
+colvars:     # extendedMass = 150000
+colvars:     # outputEnergy = off [default]
+colvars:     # extendedLangevinDamping = 1000
+colvars:     # reflectingLowerBoundary = on
+colvars:     # reflectingUpperBoundary = on
+colvars:     # outputValue = on [default]
+colvars:     # outputVelocity = off [default]
+colvars:     # outputTotalForce = off [default]
+colvars:     # outputAppliedForce = off [default]
+colvars:     # subtractAppliedForce = off [default]
+colvars:     # runAve = off [default]
+colvars:     # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "abf" instance.
+colvars:   # name = "abf1" [default]
+colvars:   # colvars = { lambda }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # applyBias = on [default]
+colvars:   # hideJacobian = off [default]
+colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
+colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
+colvars:   # inputPrefix =  [default]
+colvars:   # historyFreq = 0 [default]
+colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
+colvars:   # maxForce =  [default]
+colvars:   # integrate = on [default]
+colvars:   Finished ABF setup.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - BAOA integrator:
+colvars:   BouRabee2010 https://doi.org/10.1137/090758842
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - ABF colvar bias implementation:
+colvars: - Internal-forces free energy estimator:
+colvars:   Henin2010 https://doi.org/10.1021/ct9004432
+colvars: 
+colvars: - NAMD engine:
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 300 K).
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 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 = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars:   Initializing extended coordinate to colvar value.
+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".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Saving collective variables state to "test.tmp.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped

@@ -0,0 +1,25 @@
+configuration {
+  step           20
+  dt 1.000000e+00
+}
+
+colvar {
+  name lambda
+  x     0.017939564860453
+  extended_x     0.017939564860453
+  extended_v   -0.0039272175432668
+}
+
+abf {
+  configuration {
+step 20
+name abf1
+  }
+
+samples
+ 20
+
+gradient
+ -21.07662231815
+}
+

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj

@@ -0,0 +1,22 @@
+# step         lambda                
+           0    0.00000000000000e+00 
+           1    1.58189758101320e-04 
+           2    1.19327841511289e-03 
+           3    3.70857622331628e-03 
+           4    6.04081163026493e-03 
+           5    7.98098139879974e-03 
+           6    9.47926305485469e-03 
+           7    1.01202609943538e-02 
+           8    1.01712183611063e-02 
+           9    9.05055355392043e-03 
+          10    8.89176211928347e-03 
+          11    1.05872292938942e-02 
+          12    1.28132662393818e-02 
+          13    1.40183748162680e-02 
+          14    1.51097870579963e-02 
+          15    1.81395457523218e-02 
+          16    2.07363948627074e-02 
+          17    2.15663253895955e-02 
+          18    2.19450610288923e-02 
+          19    2.09442028306918e-02 
+          20    1.79395648604526e-02 

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.count

@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01                     20

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.grad

@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01  -2.10766223181505e+01

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.pmf

@@ -0,0 +1,5 @@
+# 1
+# -5.00000000000000e-01  1.00000000000000e+00          2  0
+
+  0.00000000000000e+00   2.10766223181505e+01
+  1.00000000000000e+00   0.00000000000000e+00

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out

@@ -0,0 +1,124 @@
+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: 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 restart output state file will be "test.restart.tmp.colvars.state".
+colvars: The final output state file will be "test.restart.colvars.state".
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "test.in":
+colvars: # units = "" [default]
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 10 [default]
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "lambda"
+colvars:   Initializing a new "alchLambda" component.
+colvars:   Warning: cannot cite unknown feature "alchLambda colvar 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:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0
+colvars:   # upperBoundary = 1
+colvars:   # hardLowerBoundary = off [default]
+colvars:   # hardUpperBoundary = off [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = on
+colvars:     Enabling the extended Lagrangian term for colvar "lambda".
+colvars:     # extendedTemp = 300 [default]
+colvars:     # extendedMass = 150000
+colvars:     # outputEnergy = off [default]
+colvars:     # extendedLangevinDamping = 1000
+colvars:     # reflectingLowerBoundary = on
+colvars:     # reflectingUpperBoundary = on
+colvars:     # outputValue = on [default]
+colvars:     # outputVelocity = off [default]
+colvars:     # outputTotalForce = off [default]
+colvars:     # outputAppliedForce = off [default]
+colvars:     # subtractAppliedForce = off [default]
+colvars:     # runAve = off [default]
+colvars:     # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "abf" instance.
+colvars:   # name = "abf1" [default]
+colvars:   # colvars = { lambda }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # applyBias = on [default]
+colvars:   # hideJacobian = off [default]
+colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
+colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
+colvars:   # inputPrefix =  [default]
+colvars:   # historyFreq = 0 [default]
+colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
+colvars:   # maxForce =  [default]
+colvars:   # integrate = on [default]
+colvars:   Finished ABF setup.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - BAOA integrator:
+colvars:   BouRabee2010 https://doi.org/10.1137/090758842
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - ABF colvar bias implementation:
+colvars: - Internal-forces free energy estimator:
+colvars:   Henin2010 https://doi.org/10.1021/ct9004432
+colvars: 
+colvars: - NAMD engine:
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 300 K).
+colvars: ----------------------------------------------------------------------
+colvars: Loading state from text file "test.colvars.state".
+colvars:   Restarting collective variable "lambda" from value: 0.0179396
+colvars:   Restarted abf bias "abf1" with step number 20.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 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 = 20, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: The restart output state file will be "test.restart.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Saving collective variables state to "test.restart.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Saving collective variables state to "test.restart.tmp.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped

@@ -0,0 +1,25 @@
+configuration {
+  step           40
+  dt 1.000000e+00
+}
+
+colvar {
+  name lambda
+  x      0.02273484988199
+  extended_x      0.02273484988199
+  extended_v   -0.0039050494285154
+}
+
+abf {
+  configuration {
+step 40
+name abf1
+  }
+
+samples
+ 40
+
+gradient
+ -22.446008885682
+}
+

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj

@@ -0,0 +1,22 @@
+# step         lambda                
+          20    1.79395648604530e-02 
+          21    1.49992941052693e-02 
+          22    1.21946330562864e-02 
+          23    1.09929345082144e-02 
+          24    1.18495428543575e-02 
+          25    1.31445493932408e-02 
+          26    1.43077987902124e-02 
+          27    1.47517911806093e-02 
+          28    1.46807494197067e-02 
+          29    1.34898108165063e-02 
+          30    1.33035794715814e-02 
+          31    1.50108946364389e-02 
+          32    1.72664594652867e-02 
+          33    1.85065811567009e-02 
+          34    1.96374992188600e-02 
+          35    2.27101696863379e-02 
+          36    2.53525217024379e-02 
+          37    2.62294494632504e-02 
+          38    2.66547145690537e-02 
+          39    2.56982742031037e-02 
+          40    2.27348498819902e-02 

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count

@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01                     40

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad

@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01  -2.24460088856819e+01

namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf

@@ -0,0 +1,5 @@
+# 1
+# -5.00000000000000e-01  1.00000000000000e+00          2  0
+
+  0.00000000000000e+00   2.24460088856819e+01
+  1.00000000000000e+00   0.00000000000000e+00

namd/tests/interface/009_lambda_dynamics/alchemy.tcl

@@ -0,0 +1,11 @@
+
+langevin                on
+langevinTemp            300.0
+langevinDamping         0.000000001
+
+alch on
+alchType TI
+alchFile ../Common/da.pdb
+alchCol  B
+alchLambda 0
+