diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 383d9b2ff..56ec3c538 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -1680,6 +1680,16 @@ 3-dimensional unit vector $\mathbf{d} = (d_{x}, d_{y}, d_{z})$, with $|\mathbf{d}| = 1$. +This multi-dimensional variable has two intrinsic degrees of freedom: however, these cannot be +sampled independently as one-dimensional variables. A decomposition in two dimensions can be done +using \refkey{polarTheta}{colvar|polarTheta} and \refkey{polarPhi}{colvar|polarPhi} angles, with the +caveat that the latter is ill-defined when the former approaches 0$^\circ$ or 180$^\circ$. + +The distance between two values of \texttt{distanceDir} is calculated internally as the angle (in +radians) between the two unit vectors: this definition adapts the standard Euclidean distance to the +unit sphere, to ensure that restraint forces comply with the mathematical constraint. + + \begin{cvcoptions} \item % \dupkey{group1}{\texttt{distanceDir}}{colvar|distance|group1}{\texttt{distance} component} @@ -1841,6 +1851,10 @@ } \end{cvcoptions} +\textbf{Note:} \texttt{polarPhi} is ill-defined when the corresponding +\refkey{polarTheta}{colvar|polarTheta} component is close to 0$^\circ$ or 180$^\circ$; please take +measures to avoid sampling these configurations in your simulations. + \cvsubsec{Contacts}{sec:cvc_contacts} diff --git a/doc/cv_version.tex b/doc/cv_version.tex index 1adc138b4..8c39576dc 100644 --- a/doc/cv_version.tex +++ b/doc/cv_version.tex @@ -1 +1 @@ -\newcommand{\cvversion}{2024-10-05} +\newcommand{\cvversion}{2024-10-11} diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 202bd8fc2..a900d0ece 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,8 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -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: 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 = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.dat": +colvars: Start colvars Initialization. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration: colvars: # units = "" [default] colvars: # indexFile = "index.ndx" colvars: The following index groups are currently defined: @@ -39,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # defaultInputStateFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -52,27 +62,27 @@ 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -81,6 +91,8 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.05 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -96,7 +108,9 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] 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] @@ -104,6 +118,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.004184 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 1.6736 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -111,14 +126,33 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +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.restart.colvars.state". +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - GROMACS engine: +colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001 +colvars: +colvars: - Colvars module: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Colvars-GROMACS interface: +colvars: n/a +colvars: colvars: The final output state file will be "test.colvars.state". -colvars: Writing to colvar trajectory file "test.colvars.traj". +colvars: ---------------------------------------------------------------------- +colvars: End colvars Initialization. +colvars: colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "test.restart.colvars.state". colvars: Saving collective variables state to "test.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index 5ac29d230..aa39775bc 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10873900278629e-01 , 2.11404356508760e-01 , 9.26642118713945e-01 ) + x ( -0.31072415075366 , 0.21141910170627 , 0.92668897995613 ) } restraint { diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index e3f559e6e..0ce14deb0 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.30999991751307e-01 , 2.15045331613065e-01 , 9.18800582722966e-01 ) ( 1.11378079309749e+00 , -1.79949933493813e-01 , -7.68852327622578e-01 ) - 1 ( -3.30676782623034e-01 , 2.14698535143340e-01 , 9.18998043763632e-01 ) ( 1.11351033169895e+00 , -1.79659734207947e-01 , -7.69017563021407e-01 ) - 2 ( -3.30191403005998e-01 , 2.14462736921122e-01 , 9.19227595241370e-01 ) ( 1.11310416603542e+00 , -1.79462418255595e-01 , -7.69209651697978e-01 ) - 3 ( -3.29533211726495e-01 , 2.14332340128698e-01 , 9.19494160038103e-01 ) ( 1.11255339157273e+00 , -1.79353302219695e-01 , -7.69432713119884e-01 ) - 4 ( -3.28699065044950e-01 , 2.14296691491131e-01 , 9.19800985352011e-01 ) ( 1.11185537762961e+00 , -1.79323471439779e-01 , -7.69689464542563e-01 ) - 5 ( -3.27691809220709e-01 , 2.14340183139530e-01 , 9.20150185600900e-01 ) ( 1.11101250595589e+00 , -1.79359865251159e-01 , -7.69981675310833e-01 ) - 6 ( -3.26525129028752e-01 , 2.14443440602006e-01 , 9.20540792629816e-01 ) ( 1.11003622797126e+00 , -1.79446271095758e-01 , -7.70308535272630e-01 ) - 7 ( -3.25217572887825e-01 , 2.14582843113291e-01 , 9.20971081916457e-01 ) ( 1.10894206499253e+00 , -1.79562923117202e-01 , -7.70668601347691e-01 ) - 8 ( -3.23796263922000e-01 , 2.14733052597090e-01 , 9.21436756154480e-01 ) ( 1.10775271364993e+00 , -1.79688618413245e-01 , -7.71058277550068e-01 ) - 9 ( -3.22293975019040e-01 , 2.14868365689500e-01 , 9.21931764878697e-01 ) ( 1.10649559829593e+00 , -1.79801848408974e-01 , -7.71472500850494e-01 ) - 10 ( -3.20748009323535e-01 , 2.14964773113452e-01 , 9.22448297106820e-01 ) ( 1.10520193420193e+00 , -1.79882522141337e-01 , -7.71904735018987e-01 ) - 11 ( -3.19198435198377e-01 , 2.15001638188676e-01 , 9.22977060680867e-01 ) ( 1.10390525057400e+00 , -1.79913370836284e-01 , -7.72347204377750e-01 ) - 12 ( -3.17687450297880e-01 , 2.14963188528407e-01 , 9.23507179994250e-01 ) ( 1.10264085840927e+00 , -1.79881196160571e-01 , -7.72790808219188e-01 ) - 13 ( -3.16255639572676e-01 , 2.14838833224103e-01 , 9.24027405533723e-01 ) ( 1.10144271919442e+00 , -1.79777135641929e-01 , -7.73226132950619e-01 ) - 14 ( -3.14940757321082e-01 , 2.14622576848283e-01 , 9.24526618808256e-01 ) ( 1.10034242572628e+00 , -1.79596172306643e-01 , -7.73643874618749e-01 ) - 15 ( -3.13776600500665e-01 , 2.14312729450493e-01 , 9.24994215643387e-01 ) ( 1.09936825929896e+00 , -1.79336892004173e-01 , -7.74035159650386e-01 ) - 16 ( -3.12790221304842e-01 , 2.13909196084839e-01 , 9.25421597590204e-01 ) ( 1.09854285718789e+00 , -1.78999215283794e-01 , -7.74392792863483e-01 ) - 17 ( -3.12001315008454e-01 , 2.13413876158312e-01 , 9.25802191019269e-01 ) ( 1.09788270039907e+00 , -1.78584731569276e-01 , -7.74711273444924e-01 ) - 18 ( -3.11419714960486e-01 , 2.12830151072677e-01 , 9.26132327439395e-01 ) ( 1.09739601747894e+00 , -1.78096270417616e-01 , -7.74987531601286e-01 ) - 19 ( -3.11047010203215e-01 , 2.12159472204629e-01 , 9.26411418214119e-01 ) ( 1.09708413813805e+00 , -1.77535046340834e-01 , -7.75221074761574e-01 ) - 20 ( -3.10873900278629e-01 , 2.11404356508760e-01 , 9.26642118713945e-01 ) ( 1.09693927975316e+00 , -1.76903165526531e-01 , -7.75414124939829e-01 ) + 0 ( -3.30999991751309e-01 , 2.15045331613065e-01 , 9.18800582722965e-01 ) ( 3.38426402875894e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 1 ( -3.30675795098964e-01 , 2.14698617732066e-01 , 9.18998379802493e-01 ) ( 3.38324723101736e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 2 ( -3.30188451860992e-01 , 2.14462983804546e-01 , 9.19228597703146e-01 ) ( 3.38172018810604e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 3 ( -3.29527387032144e-01 , 2.14332839495249e-01 , 9.19496131100980e-01 ) ( 3.37965156710645e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 4 ( -3.28689451157889e-01 , 2.14297521833692e-01 , 9.19804227449224e-01 ) ( 3.37703403459308e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 5 ( -3.27677536797495e-01 , 2.14341420707726e-01 , 9.20154980015497e-01 ) ( 3.37387980157688e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 6 ( -3.26505348637980e-01 , 2.14445150909860e-01 , 9.20547410273930e-01 ) ( 3.37023520560286e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 7 ( -3.25191560545378e-01 , 2.14585104624817e-01 , 9.20979740180650e-01 ) ( 3.36616206137160e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 8 ( -3.23763332951352e-01 , 2.14735934351762e-01 , 9.21447655992628e-01 ) ( 3.36174810134456e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 9 ( -3.22253503391576e-01 , 2.14871933826910e-01 , 9.21945080579825e-01 ) ( 3.35709770231332e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 10 ( -3.20699438120479e-01 , 2.14969090747406e-01 , 9.22464178389840e-01 ) ( 3.35232786829431e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 11 ( -3.19141265367702e-01 , 2.15006765357427e-01 , 9.22995635737265e-01 ) ( 3.34756245411490e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 12 ( -3.17621238055519e-01 , 2.14969182199493e-01 , 9.23528559298823e-01 ) ( 3.34293003545057e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 13 ( -3.16179990781952e-01 , 2.14845747479523e-01 , 9.24051685902412e-01 ) ( 3.33855252183575e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 14 ( -3.14855323489180e-01 , 2.14630463673023e-01 , 9.24553886657791e-01 ) ( 3.33454174945745e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 15 ( -3.13681063673994e-01 , 2.14321640725317e-01 , 9.25024553516911e-01 ) ( 3.33099645805029e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 16 ( -3.12684301431285e-01 , 2.13919183582479e-01 , 9.25455082936949e-01 ) ( 3.32799446637915e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 17 ( -3.11884757522437e-01 , 2.13424990715836e-01 , 9.25838901409482e-01 ) ( 3.32559134179721e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 18 ( -3.11292307607676e-01 , 2.12842414436210e-01 , 9.26172341328142e-01 ) ( 3.32381346606555e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 19 ( -3.10908528232233e-01 , 2.12172951215445e-01 , 9.26454815867992e-01 ) ( 3.32266305791510e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 20 ( -3.10724150753660e-01 , 2.11419101706274e-01 , 9.26688979956128e-01 ) ( 3.32211072705070e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 0290bbafc..785277a9f 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,8 +1,17 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -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: 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 = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available colvars: ---------------------------------------------------------------------- -colvars: Reading new configuration from file "test.dat": +colvars: Start colvars Initialization. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration: colvars: # units = "" [default] colvars: # indexFile = "index.ndx" colvars: The following index groups are currently defined: @@ -39,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # defaultInputStateFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -52,27 +62,27 @@ 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. @@ -81,6 +91,8 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.05 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -96,7 +108,9 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] 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] @@ -104,6 +118,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.004184 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 1.6736 according to the specified width (0.05). colvars: ---------------------------------------------------------------------- @@ -111,19 +126,38 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +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: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - GROMACS engine: +colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001 +colvars: +colvars: - Colvars module: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Colvars-GROMACS interface: +colvars: n/a +colvars: +colvars: The final output state file will be "test.restart.part0002.colvars.state". colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state.dat". -colvars: Restarting collective variable "one" from value: ( -0.310874 , 0.211404 , 0.926642 ) +colvars: Loading state from unformatted memory. +colvars: Restarting collective variable "one" from value: ( -0.310724 , 0.211419 , 0.926689 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.part0002.restart.colvars.state". -colvars: The final output state file will be "test.restart.part0002.colvars.state". -colvars: Writing to colvar trajectory file "test.restart.part0002.colvars.traj". -colvars: Initializing step number to 20. +colvars: ---------------------------------------------------------------------- +colvars: End colvars Initialization. +colvars: colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". -colvars: Saving collective variables state to "test.restart.part0002.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". -colvars: Saving collective variables state to "test.restart.part0002.restart.colvars.state". colvars: Saving collective variables state to "test.restart.part0002.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". +colvars: Saving collective variables state to "test.restart.part0002.colvars.state". +colvars: Saving collective variables state to "test.restart.part0002.colvars.state". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index a9643ab56..6e0b95ce8 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08593864856337e-01 , 1.95821811443888e-01 , 9.30818803385419e-01 ) + x ( -0.30817666194887 , 0.1958681474458 , 0.93094726695243 ) } restraint { diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index dfb54c4bd..5284c8d56 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10873900278629e-01 , 2.11404356508760e-01 , 9.26642118713945e-01 ) ( 1.09693927975316e+00 , -1.76903165526531e-01 , -7.75414124939829e-01 ) - 21 ( -3.10883853126719e-01 , 2.10567919487789e-01 , 9.26829208186529e-01 ) ( 1.09694760829644e+00 , -1.76203235027382e-01 , -7.75570681410487e-01 ) - 22 ( -3.11049991351596e-01 , 2.09654548979040e-01 , 9.26980513804129e-01 ) ( 1.09708663276302e+00 , -1.75438926585661e-01 , -7.75697293951295e-01 ) - 23 ( -3.11341443297634e-01 , 2.08671214998594e-01 , 9.27104540877865e-01 ) ( 1.09733051975146e+00 , -1.74616072710824e-01 , -7.75801079806597e-01 ) - 24 ( -3.11723074231696e-01 , 2.07627794106425e-01 , 9.27210560825339e-01 ) ( 1.09764986851708e+00 , -1.73742938108257e-01 , -7.75889797298644e-01 ) - 25 ( -3.12158273431782e-01 , 2.06537342469155e-01 , 9.27307682753609e-01 ) ( 1.09801404320771e+00 , -1.72830448178189e-01 , -7.75971068928220e-01 ) - 26 ( -3.12609997183346e-01 , 2.05415663605210e-01 , 9.27404655372540e-01 ) ( 1.09839204564302e+00 , -1.71891827304840e-01 , -7.76052215615741e-01 ) - 27 ( -3.13043637307834e-01 , 2.04280658881946e-01 , 9.27509080035252e-01 ) ( 1.09875491569920e+00 , -1.70942055352412e-01 , -7.76139598173499e-01 ) - 28 ( -3.13427537160295e-01 , 2.03151611859531e-01 , 9.27627404483344e-01 ) ( 1.09907616309573e+00 , -1.69997268804055e-01 , -7.76238612071663e-01 ) - 29 ( -3.13734134816361e-01 , 2.02047600274335e-01 , 9.27764873162598e-01 ) ( 1.09933272401433e+00 , -1.69073431909563e-01 , -7.76353645862462e-01 ) - 30 ( -3.13941154495898e-01 , 2.00987177816775e-01 , 9.27925161781397e-01 ) ( 1.09950595808217e+00 , -1.68186070397077e-01 , -7.76487775378673e-01 ) - 31 ( -3.14030994670674e-01 , 1.99987700405082e-01 , 9.28110690636001e-01 ) ( 1.09958113634042e+00 , -1.67349707698973e-01 , -7.76643025924205e-01 ) - 32 ( -3.13990535521189e-01 , 1.99065199194795e-01 , 9.28322675621281e-01 ) ( 1.09954728012413e+00 , -1.66577758686204e-01 , -7.76820414959888e-01 ) - 33 ( -3.13811179751699e-01 , 1.98234215093668e-01 , 9.28561112382510e-01 ) ( 1.09939719521622e+00 , -1.65882391190381e-01 , -7.77019938841684e-01 ) - 34 ( -3.13488342086411e-01 , 1.97508066400127e-01 , 9.28824861361277e-01 ) ( 1.09912704465791e+00 , -1.65274749963627e-01 , -7.77240643987117e-01 ) - 35 ( -3.13019919852056e-01 , 1.96898397632424e-01 , 9.29112237991512e-01 ) ( 1.09873506893220e+00 , -1.64764579138812e-01 , -7.77481120751297e-01 ) - 36 ( -3.12407184423245e-01 , 1.96414771631671e-01 , 9.29420781242608e-01 ) ( 1.09822233192537e+00 , -1.64359880901382e-01 , -7.77739309743814e-01 ) - 37 ( -3.11652773450002e-01 , 1.96063917381024e-01 , 9.29748078299777e-01 ) ( 1.09759104082296e+00 , -1.64066286064441e-01 , -7.78013191921254e-01 ) - 38 ( -3.10761279956207e-01 , 1.95849238240613e-01 , 9.30091663633511e-01 ) ( 1.09684503906735e+00 , -1.63886642559745e-01 , -7.78300704128522e-01 ) - 39 ( -3.09739056531641e-01 , 1.95770115568982e-01 , 9.30449234890865e-01 ) ( 1.09598964250568e+00 , -1.63820432708124e-01 , -7.78599919756676e-01 ) - 40 ( -3.08593864856337e-01 , 1.95821811443888e-01 , 9.30818803385419e-01 ) ( 1.09503134611178e+00 , -1.63863691816245e-01 , -7.78909174672918e-01 ) + 20 ( -3.10724150753660e-01 , 2.11419101706274e-01 , 9.26688979956128e-01 ) ( 3.32211072705070e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 21 ( -3.10722637481973e-01 , 2.10583980160159e-01 , 9.26879619937860e-01 ) ( 3.32210619476656e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 ( -3.10877135088908e-01 , 2.09671975774600e-01 , 9.27034556774281e-01 ) ( 3.32256899870771e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 23 ( -3.11156771498279e-01 , 2.08690057256423e-01 , 9.27162296231398e-01 ) ( 3.32340707215601e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 ( -3.11526414791607e-01 , 2.07648099145394e-01 , 9.27272106670093e-01 ) ( 3.32451571071889e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 25 ( -3.11949455095936e-01 , 2.06559154362725e-01 , 9.27373092781058e-01 ) ( 3.32578563634033e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 ( -3.12388847434885e-01 , 2.05439021980326e-01 , 9.27473997611831e-01 ) ( 3.32710593723229e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 27 ( -3.12809980850511e-01 , 2.04305597836951e-01 , 9.27582416054115e-01 ) ( 3.32837260684817e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 ( -3.13181194024425e-01 , 2.03178159237175e-01 , 9.27704788884066e-01 ) ( 3.32949013105527e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 29 ( -3.13474918339783e-01 , 2.02075777359962e-01 , 9.27846353539331e-01 ) ( 3.33037504458960e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 ( -3.13668869410699e-01 , 2.01016999575102e-01 , 9.28010779163926e-01 ) ( 3.33095969104440e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 31 ( -3.13745434737153e-01 , 2.00019176206034e-01 , 9.28200480139638e-01 ) ( 3.33119056053970e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 ( -3.13691480974416e-01 , 1.99098333881233e-01 , 9.28416667348123e-01 ) ( 3.33102786812914e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 33 ( -3.13498394796557e-01 , 1.98269010145880e-01 , 9.28659332627286e-01 ) ( 3.33044579837917e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 ( -3.13161572624239e-01 , 1.97544521088611e-01 , 9.28927333874606e-01 ) ( 3.32943103797579e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 35 ( -3.12678891449374e-01 , 1.96936509818729e-01 , 9.29218984923580e-01 ) ( 3.32797819140519e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 ( -3.12051601211012e-01 , 1.96454538216848e-01 , 9.29531824412510e-01 ) ( 3.32609245125784e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 37 ( -3.11282317383170e-01 , 1.96105334367771e-01 , 9.29863439821713e-01 ) ( 3.32378350694454e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 ( -3.10375610877295e-01 , 1.95892300700812e-01 , 9.30211366678933e-01 ) ( 3.32106725105046e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 39 ( -3.09337813221428e-01 , 1.95814817676749e-01 , 9.30573304199947e-01 ) ( 3.31796509876705e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 ( -3.08176661948874e-01 , 1.95868147445796e-01 , 9.30947266952431e-01 ) ( 3.31450281613893e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/gromacs-version.txt b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/gromacs-version.txt index 30e5ca48b..e69de29bb 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/gromacs-version.txt +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/gromacs-version.txt @@ -1,3 +0,0 @@ - :-) GROMACS - gmx mdrun, 2020.3-MODIFIED (double precision) (-: -colvars: Initializing the collective variables module, version "2019-12-05". -colvars: This version was built with the C++11 standard or higher.colvars: Using GROMACS interface, version "2019-05-06". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index e69de29bb..a765c9e43 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -0,0 +1,162 @@ +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 = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available +colvars: ---------------------------------------------------------------------- +colvars: Start colvars Initialization. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration: +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # defaultInputStateFile = "" [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distanceDir" 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: # 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: # 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: # 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 = 0.05 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +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 "harmonic" instance. +colvars: # name = "harmonic1" [default] +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = on +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { ( 1 , 0 , 0 ) } +colvars: # targetCenters = { ( -0.707107 , 0.707107 , 0 ) } +colvars: Initial step for restraint change: 0 +colvars: # targetNumSteps = 10 +colvars: # targetNumStages = 0 [default] +colvars: # outputAccumulatedWork = on +colvars: # outputCenters = on +colvars: # forceConstant = 0.004184 +colvars: # decoupling = off [default] +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 1.6736 according to the specified width (0.05). +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +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: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - GROMACS engine: +colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001 +colvars: +colvars: - Colvars module: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Colvars-GROMACS interface: +colvars: n/a +colvars: +colvars: The final output state file will be "test.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: End colvars Initialization. +colvars: +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.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped index 668eb79a8..279745a31 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) + x ( -0.31085916407103 , 0.21148785049618 , 0.92662801015594 ) } restraint { configuration { step 20 name harmonic1 - firstStep 0 - centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) - accumulatedWork -5.55059495927072e-01 +firstStep 0 +centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) +accumulatedWork -2.52812949338518e+01 } } diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj index a0e19b09e..c1c7d78ce 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 0 ( -3.30999991751309e-01 , 2.15045331613065e-01 , 9.18800582722965e-01 ) ( 1.11378079309750e+00 , -1.79949933493813e-01 , -7.68852327622577e-01 ) 2.22756158619499e+00 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( -3.30676782623035e-01 , 2.14698535143340e-01 , 9.18998043763632e-01 ) ( 1.11048488664575e+00 , -1.08566615530599e-01 , -7.69017563021407e-01 ) 2.19449259764792e+00 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -1.72056748042513e-02 - 2 ( -3.30191402709992e-01 , 2.14462744628538e-01 , 9.19227593549499e-01 ) ( 1.09445346557288e+00 , -3.77530718922370e-03 , -7.69209650282220e-01 ) 2.13853504700783e+00 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -4.66529868068846e-02 - 3 ( -3.29533211475485e-01 , 2.14332374411399e-01 , 9.19494152136829e-01 ) ( 1.04314868322252e+00 , 1.54321220161941e-01 , -7.69432706508098e-01 ) 2.03632995237275e+00 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -1.00805936302149e-01 - 4 ( -3.28699069057470e-01 , 2.14296787722334e-01 , 9.19800961497998e-01 ) ( 8.99582104322054e-01 , 3.77633009931505e-01 , -7.69689444581524e-01 ) 1.84545470089225e+00 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -1.99926587941052e-01 - 5 ( -3.27691834282163e-01 , 2.14340399151662e-01 , 9.20150126357812e-01 ) ( 5.94442023130421e-01 , 5.93742346795334e-01 , -7.69981625736217e-01 ) 1.55205903108605e+00 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -3.39925761052374e-01 - 6 ( -3.26525219575073e-01 , 2.14443853732057e-01 , 9.20540664271815e-01 ) ( 2.25456984382301e-01 , 6.55988226043346e-01 , -7.70308427862655e-01 ) 1.28408996002688e+00 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -4.54082888609383e-01 - 7 ( -3.25217810308112e-01 , 2.14583532852425e-01 , 9.20970837370527e-01 ) ( -3.45446132883389e-02 , 5.99010452204356e-01 , -7.70668396711657e-01 ) 1.13998163222684e+00 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -5.12696099304228e-01 - 8 ( -3.23796753972870e-01 , 2.14734087750040e-01 , 9.21436342714346e-01 ) ( -1.83336242013975e-01 , 5.23058985434512e-01 , -7.71057931583365e-01 ) 1.07759705274523e+00 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -5.38347687996117e-01 - 9 ( -3.22294835838418e-01 , 2.14869803103587e-01 , 9.21931128938661e-01 ) ( -2.69600896841635e-01 , 4.60035016859046e-01 , -7.71471968695871e-01 ) 1.05101082552318e+00 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -5.49741754293482e-01 - 10 ( -3.20749363670832e-01 , 2.14966659531062e-01 , 9.22447386572705e-01 ) ( -3.23303886977151e-01 , 4.11822853801310e-01 , -7.71903973084039e-01 ) 1.03962620687203e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 11 ( -3.19200405834927e-01 , 2.15004012199105e-01 , 9.22975826147741e-01 ) ( -3.24600054894236e-01 , 4.11791597088692e-01 , -7.72346171320430e-01 ) 1.04141506145259e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 12 ( -3.17690153264675e-01 , 2.14966086384984e-01 , 9.23505575631783e-01 ) ( -3.25863834245023e-01 , 4.11823333409948e-01 , -7.72789465688676e-01 ) 1.04324719728625e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 13 ( -3.16259183478589e-01 , 2.14842289084984e-01 , 9.24025389091761e-01 ) ( -3.27061269762020e-01 , 4.11926926990588e-01 , -7.73224445591986e-01 ) 1.04508713028118e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 14 ( -3.14945243314928e-01 , 2.14626623157147e-01 , 9.24524151304584e-01 ) ( -3.28160774890971e-01 , 4.12107396239002e-01 , -7.73641809811676e-01 ) 1.04689728740514e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 15 ( -3.13782120484417e-01 , 2.14317396540321e-01 , 9.24991261798987e-01 ) ( -3.29134076075543e-01 , 4.12366157071962e-01 , -7.74032687873392e-01 ) 1.04863968622001e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 16 ( -3.12796860422836e-01 , 2.13914513281047e-01 , 9.25418124480686e-01 ) ( -3.29958541695074e-01 , 4.12703289783323e-01 , -7.74389886565438e-01 ) 1.05028243433359e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 17 ( -3.12009150054690e-01 , 2.13419871583257e-01 , 9.25798168444686e-01 ) ( -3.30617697731138e-01 , 4.13117205956034e-01 , -7.74707907354513e-01 ) 1.05179998760465e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 18 ( -3.11428813565447e-01 , 2.12836854235221e-01 , 9.26127727454735e-01 ) ( -3.31103323305337e-01 , 4.13605074872870e-01 , -7.74983682334123e-01 ) 1.05317671671676e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 19 ( -3.11057435290019e-01 , 2.12166908276454e-01 , 9.26406214888051e-01 ) ( -3.31414092646215e-01 , 4.14165685651166e-01 , -7.75216720618321e-01 ) 1.05440903429928e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 20 ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) ( -3.31557794912004e-01 , 4.14796931575128e-01 , -7.75409245854786e-01 ) 1.05550497653936e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 0 ( -3.30999991751309e-01 , 2.15045331613065e-01 , 9.18800582722965e-01 ) ( 3.38426402875894e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 3.04684940271844e+00 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( -3.30675795098964e-01 , 2.14698617732066e-01 , 9.18998379802493e-01 ) ( 3.31163937209541e+00 , 2.82372218605279e-01 , 0.00000000000000e+00 ) 2.98057905225948e+00 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -3.31563622325896e+00 + 2 ( -3.30188467095213e-01 , 2.14463077754792e-01 , 9.19228570311680e-01 ) ( 3.15510994911585e+00 , 6.77519582980243e-01 , 0.00000000000000e+00 ) 2.87107994832291e+00 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -6.52544882677179e+00 + 3 ( -3.29527469842356e-01 , 2.14333250256405e-01 , 9.19496005675838e-01 ) ( 2.81300149062219e+00 , 1.22313365679647e+00 , 0.00000000000000e+00 ) 2.67897652696889e+00 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -9.55241697586774e+00 + 4 ( -3.28689747860648e-01 , 2.14298645630427e-01 , 9.19803859598484e-01 ) ( 2.10159215847126e+00 , 1.87421210231479e+00 , 0.00000000000000e+00 ) 2.34397826661473e+00 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -1.22726943175312e+01 + 5 ( -3.27678398494208e-01 , 2.14343848901894e-01 , 9.20154107526665e-01 ) ( 9.62013365533624e-01 , 2.32250571425546e+00 , 0.00000000000000e+00 ) 1.87803706343684e+00 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -1.46146682920846e+01 + 6 ( -3.26507450158953e-01 , 2.14449580466058e-01 , 9.20545632996339e-01 ) ( -1.31261398356140e-01 , 2.29514248383312e+00 , 0.00000000000000e+00 ) 1.49337652196477e+00 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.67563718529002e+01 + 7 ( -3.25195922645399e-01 , 2.14592181044706e-01 , 9.20976551128900e-01 ) ( -8.06534629945617e-01 , 2.04751784914132e+00 , 0.00000000000000e+00 ) 1.29974197963183e+00 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.88822756004184e+01 + 8 ( -3.23771158873574e-01 , 2.14746179117133e-01 , 9.21442518682666e-01 ) ( -1.17328978667786e+00 , 1.81498327875003e+00 , 0.00000000000000e+00 ) 1.21846032286028e+00 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -2.10149754520754e+01 + 9 ( -3.22266073341863e-01 , 2.14885757969215e-01 , 9.21937464796183e-01 ) ( -1.38233911230013e+00 , 1.64004775417763e+00 , 0.00000000000000e+00 ) 1.18426368897500e+00 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -2.31484337646817e+01 + 10 ( -3.20718044577649e-01 , 2.14986818712036e-01 , 9.22453578052775e-01 ) ( -1.51180850991670e+00 , 1.51180850991670e+00 , 0.00000000000000e+00 ) 1.16969980593972e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 11 ( -3.19167175358182e-01 , 2.15028654363293e-01 , 9.22981577268252e-01 ) ( -1.51256984177381e+00 , 1.51256984177381e+00 , 0.00000000000000e+00 ) 1.17198175005017e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 12 ( -3.17655640337977e-01 , 2.14995471205116e-01 , 9.23510607152273e-01 ) ( -1.51335014487906e+00 , 1.51335014487906e+00 , 0.00000000000000e+00 ) 1.17431884672886e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 13 ( -3.16223990212843e-01 , 2.14876659918937e-01 , 9.24029441649967e-01 ) ( -1.51413433568340e+00 , 1.51413433568340e+00 , 0.00000000000000e+00 ) 1.17666584553126e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 14 ( -3.14909941889115e-01 , 2.14666211292004e-01 , 9.24526985127493e-01 ) ( -1.51490635984962e+00 , 1.51490635984962e+00 , 0.00000000000000e+00 ) 1.17897472706138e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 15 ( -3.13747226460728e-01 , 2.14362419073791e-01 , 9.24992665472020e-01 ) ( -1.51564992286108e+00 , 1.51564992286108e+00 , 0.00000000000000e+00 ) 1.18119689393380e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 16 ( -3.12762860405954e-01 , 2.13965183257168e-01 , 9.25417902087706e-01 ) ( -1.51635124986036e+00 , 1.51635124986036e+00 , 0.00000000000000e+00 ) 1.18329140308997e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 17 ( -3.11976478680631e-01 , 2.13476395624341e-01 , 9.25796146709022e-01 ) ( -1.51699925158927e+00 , 1.51699925158927e+00 , 0.00000000000000e+00 ) 1.18522542082430e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 18 ( -3.11397857391711e-01 , 2.12899437008971e-01 , 9.26123752061848e-01 ) ( -1.51758706455595e+00 , 1.51758706455595e+00 , 0.00000000000000e+00 ) 1.18697877425327e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 19 ( -3.11028536021993e-01 , 2.12235749785969e-01 , 9.26400149121751e-01 ) ( -1.51811299861783e+00 , 1.51811299861783e+00 , 0.00000000000000e+00 ) 1.18854672634015e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 20 ( -3.10859164071033e-01 , 2.11487850496175e-01 , 9.26628010155945e-01 ) ( -1.51858037981550e+00 , 1.51858037981550e+00 , 0.00000000000000e+00 ) 1.18993946206487e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out index e69de29bb..25fdd7aa4 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out @@ -0,0 +1,167 @@ +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 = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available +colvars: ---------------------------------------------------------------------- +colvars: Start colvars Initialization. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration: +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # defaultInputStateFile = "" [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distanceDir" 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: # 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: # 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: # 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 = 0.05 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +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 "harmonic" instance. +colvars: # name = "harmonic1" [default] +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = on +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { ( 1 , 0 , 0 ) } +colvars: # targetCenters = { ( -0.707107 , 0.707107 , 0 ) } +colvars: Initial step for restraint change: 0 +colvars: # targetNumSteps = 10 +colvars: # targetNumStages = 0 [default] +colvars: # outputAccumulatedWork = on +colvars: # outputCenters = on +colvars: # forceConstant = 0.004184 +colvars: # decoupling = off [default] +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 1.6736 according to the specified width (0.05). +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +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: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - GROMACS engine: +colvars: Abraham2015 https://doi.org/10.1016/j.softx.2015.06.001 +colvars: +colvars: - Colvars module: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - Colvars-GROMACS interface: +colvars: n/a +colvars: +colvars: The final output state file will be "test.restart.part0002.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: Loading state from unformatted memory. +colvars: Restarting collective variable "one" from value: ( -0.310859 , 0.211488 , 0.926628 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: End colvars Initialization. +colvars: +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". +colvars: Saving collective variables state to "test.restart.part0002.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.part0002.colvars.traj". +colvars: Saving collective variables state to "test.restart.part0002.colvars.state". +colvars: Saving collective variables state to "test.restart.part0002.colvars.state". diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped index bdc922a18..dd33f8f2d 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x ( -3.08639969524265e-01 , 1.95850147681302e-01 , 9.30797555253167e-01 ) + x ( -0.30868184678574 , 0.19609201133499 , 0.93073274389351 ) } restraint { configuration { step 40 name harmonic1 - firstStep 0 - centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) - accumulatedWork -5.55059495927072e-01 +firstStep 0 +centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) +accumulatedWork -2.52812949338518e+01 } } diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj index fb24bade0..b44544892 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( -3.10885706960921e-01 , 2.11412551292752e-01 , 9.26636288067383e-01 ) ( -3.31557794912004e-01 , 4.14796931575128e-01 , -7.75409245854786e-01 ) 1.05550497653936e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 21 ( -3.10897091374193e-01 , 2.10576898213230e-01 , 9.26822727663689e-01 ) ( -3.31548268434978e-01 , 4.15496206072072e-01 , -7.75565258508975e-01 ) 1.05648042754375e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 22 ( -3.11064705021948e-01 , 2.09664336230821e-01 , 9.26973362833311e-01 ) ( -3.31408009334537e-01 , 4.16259837938952e-01 , -7.75691310018915e-01 ) 1.05736200976446e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 23 ( -3.11357671914477e-01 , 2.08681834875126e-01 , 9.27096700421886e-01 ) ( -3.31162854638869e-01 , 4.17081995073397e-01 , -7.75794518913034e-01 ) 1.05817801443891e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 24 ( -3.11740853393812e-01 , 2.07639270301561e-01 , 9.27202013454421e-01 ) ( -3.30842208376961e-01 , 4.17954413108557e-01 , -7.75882644858660e-01 ) 1.05895833756397e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 25 ( -3.12177635464617e-01 , 2.06549698371545e-01 , 9.27298412604241e-01 ) ( -3.30476709140112e-01 , 4.18866166899594e-01 , -7.75963311667228e-01 ) 1.05973085816301e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 26 ( -3.12630971759631e-01 , 2.05428922422296e-01 , 9.27394648102437e-01 ) ( -3.30097357328444e-01 , 4.19804032213926e-01 , -7.76043841532119e-01 ) 1.06052071553325e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 27 ( -3.13066251934311e-01 , 2.04294843741088e-01 , 9.27498322758918e-01 ) ( -3.29733114878271e-01 , 4.20753029254360e-01 , -7.76130596484663e-01 ) 1.06134768340546e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 28 ( -3.13451817595270e-01 , 2.03166745880829e-01 , 9.27615885706156e-01 ) ( -3.29410473533181e-01 , 4.21697021543826e-01 , -7.76228973158911e-01 ) 1.06222640633799e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 29 ( -3.13760105408211e-01 , 2.02063706631599e-01 , 9.27752582705393e-01 ) ( -3.29152498291312e-01 , 4.22620044787581e-01 , -7.76343361207873e-01 ) 1.06316692624188e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 30 ( -3.13968838424589e-01 , 2.01004279720987e-01 , 9.27912090681096e-01 ) ( -3.28977830503207e-01 , 4.23506573226381e-01 , -7.76476837481941e-01 ) 1.06417364922862e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 31 ( -3.14060414173331e-01 , 2.00005821063283e-01 , 9.28096831041933e-01 ) ( -3.28901199916659e-01 , 4.24342083431148e-01 , -7.76631428215889e-01 ) 1.06524686707691e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 32 ( -3.14021712205281e-01 , 1.99084361748090e-01 , 9.28308020632710e-01 ) ( -3.28933585723524e-01 , 4.25113160586101e-01 , -7.76808151665451e-01 ) 1.06638313529438e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 33 ( -3.13844134973355e-01 , 1.98254442559562e-01 , 9.28545655823247e-01 ) ( -3.29082182351199e-01 , 4.25807636963061e-01 , -7.77007004792893e-01 ) 1.06757542057160e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 34 ( -3.13523097439585e-01 , 1.97529381671397e-01 , 9.28808597477653e-01 ) ( -3.29350826559459e-01 , 4.26414367914278e-01 , -7.77227034369300e-01 ) 1.06881338799430e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 35 ( -3.13056497779899e-01 , 1.96920823570625e-01 , 9.29095161133697e-01 ) ( -3.29741277154683e-01 , 4.26923609333004e-01 , -7.77466830836678e-01 ) 1.07008574464239e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 36 ( -3.12445608882840e-01 , 1.96438331222221e-01 , 9.29402885468116e-01 ) ( -3.30252468983742e-01 , 4.27327358930148e-01 , -7.77724334559719e-01 ) 1.07137966721610e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 37 ( -3.11693070648280e-01 , 1.96088634007210e-01 , 9.29729357029793e-01 ) ( -3.30882192978423e-01 , 4.27619985559669e-01 , -7.77997525962531e-01 ) 1.07268406797811e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 38 ( -3.10803479062424e-01 , 1.95875135976297e-01 , 9.30072109306026e-01 ) ( -3.31626603217466e-01 , 4.27798640711938e-01 , -7.78284341067283e-01 ) 1.07398947957346e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 39 ( -3.09783190290509e-01 , 1.95797219440961e-01 , 9.30428838693547e-01 ) ( -3.32480380861805e-01 , 4.27863841268707e-01 , -7.78582852218760e-01 ) 1.07528911100899e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 - 40 ( -3.08639969524265e-01 , 1.95850147681302e-01 , 9.30797555253167e-01 ) ( -3.33437027998998e-01 , 4.27819550917190e-01 , -7.78891394235850e-01 ) 1.07657937834902e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -5.55059495927072e-01 + 20 ( -3.10859164071033e-01 , 2.11487850496175e-01 , 9.26628010155945e-01 ) ( -1.51858037981550e+00 , 1.51858037981550e+00 , 0.00000000000000e+00 ) 1.18993946206487e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 21 ( -3.10873156229150e-01 , 2.10658851322289e-01 , 9.26812132579036e-01 ) ( -1.51899594806485e+00 , 1.51899594806485e+00 , 0.00000000000000e+00 ) 1.19117728505514e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 22 ( -3.11043598699693e-01 , 2.09753138106964e-01 , 9.26960355550455e-01 ) ( -1.51937109694223e+00 , 1.51937109694223e+00 , 0.00000000000000e+00 ) 1.19229429624137e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 23 ( -3.11339579734293e-01 , 2.08777677821884e-01 , 9.27081197810728e-01 ) ( -1.51971798067949e+00 , 1.51971798067949e+00 , 0.00000000000000e+00 ) 1.19332679521474e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 24 ( -3.11725931375998e-01 , 2.07742343911198e-01 , 9.27183941973785e-01 ) ( -1.52004947546253e+00 , 1.52004947546253e+00 , 0.00000000000000e+00 ) 1.19431317279565e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 25 ( -3.12166014183763e-01 , 2.06660189079517e-01 , 9.27277706967142e-01 ) ( -1.52037761394650e+00 , 1.52037761394650e+00 , 0.00000000000000e+00 ) 1.19528925937385e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 26 ( -3.12622759629733e-01 , 2.05547013264352e-01 , 9.27371250093291e-01 ) ( -1.52071326888274e+00 , 1.52071326888274e+00 , 0.00000000000000e+00 ) 1.19628739156946e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 27 ( -3.13061537722483e-01 , 2.04420714035309e-01 , 9.27472180322477e-01 ) ( -1.52106501518819e+00 , 1.52106501518819e+00 , 0.00000000000000e+00 ) 1.19733303498922e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 28 ( -3.13450671971929e-01 , 2.03300570960055e-01 , 9.27586952305638e-01 ) ( -1.52143922794226e+00 , 1.52143922794226e+00 , 0.00000000000000e+00 ) 1.19844508370270e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 29 ( -3.13762581736334e-01 , 2.02205657844089e-01 , 9.27720816969194e-01 ) ( -1.52184030623188e+00 , 1.52184030623188e+00 , 0.00000000000000e+00 ) 1.19963653272339e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 30 ( -3.13974972903305e-01 , 2.01154524301222e-01 , 9.27877456210419e-01 ) ( -1.52227022161315e+00 , 1.52227022161315e+00 , 0.00000000000000e+00 ) 1.20091314495102e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 31 ( -3.14070225590611e-01 , 2.00164522246634e-01 , 9.28059296290512e-01 ) ( -1.52272917089779e+00 , 1.52272917089779e+00 , 0.00000000000000e+00 ) 1.20227540056580e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 32 ( -3.14035202418071e-01 , 1.99251679043144e-01 , 9.28267558433843e-01 ) ( -1.52321573370437e+00 , 1.52321573370437e+00 , 0.00000000000000e+00 ) 1.20371897491504e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 33 ( -3.13861290095337e-01 , 1.98430532171049e-01 , 9.28502242583186e-01 ) ( -1.52372692947072e+00 , 1.52372692947072e+00 , 0.00000000000000e+00 ) 1.20523491903694e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 34 ( -3.13543890241182e-01 , 1.97714397379498e-01 , 9.28762211742751e-01 ) ( -1.52425833414814e+00 , 1.52425833414814e+00 , 0.00000000000000e+00 ) 1.20681001818284e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 35 ( -3.13080891364439e-01 , 1.97114918049416e-01 , 9.29045781727047e-01 ) ( -1.52480509144991e+00 , 1.52480509144991e+00 , 0.00000000000000e+00 ) 1.20842979986100e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 36 ( -3.12473561584780e-01 , 1.96641657535177e-01 , 9.29350489230162e-01 ) ( -1.52536165973704e+00 , 1.52536165973704e+00 , 0.00000000000000e+00 ) 1.21007779010948e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 37 ( -3.11724541801110e-01 , 1.96301347659450e-01 , 9.29673916459944e-01 ) ( -1.52592323059771e+00 , 1.52592323059771e+00 , 0.00000000000000e+00 ) 1.21173971762892e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 38 ( -3.10838435200327e-01 , 1.96097396988595e-01 , 9.30013590275169e-01 ) ( -1.52648568108896e+00 , 1.52648568108896e+00 , 0.00000000000000e+00 ) 1.21340336784814e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 39 ( -3.09821611288606e-01 , 1.96029194202950e-01 , 9.30367198582729e-01 ) ( -1.52704603783020e+00 , 1.52704603783020e+00 , 0.00000000000000e+00 ) 1.21505994952097e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 + 40 ( -3.08681846785739e-01 , 1.96092011334989e-01 , 9.30732743893511e-01 ) ( -1.52760271795577e+00 , 1.52760271795577e+00 , 0.00000000000000e+00 ) 1.21670479744977e+00 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -2.52812949338518e+01 diff --git a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt index 1fcba9718..e69de29bb 100644 --- a/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt +++ b/gromacs/tests/library/000_distancedir_harmonic-ddir-moving/gromacs-version.txt @@ -1,3 +0,0 @@ - :-) GROMACS - gmx mdrun, 2020.7-Colvars-2023-01-31-dev-20230405-4336830f69-unknown (double precision) (-: -colvars: Initializing the collective variables module, version 2023-01-31. -colvars: Using GROMACS interface, version "2023-01-31". diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 42b38710e..0e182c70a 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,10 +1,13 @@ -colvars: Creating proxy instance 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: 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: Using LAMMPS interface, version "2020-04-07". +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -56,25 +59,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested. @@ -88,25 +91,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested. @@ -139,7 +142,7 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # zeroStepData = off [default] +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -149,6 +152,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -156,15 +160,14 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". +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 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 "rest.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Saving collective variables state to "test.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Saving collective variables state to "test.colvars.state". diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index 55a3a6bc3..2945bc222 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.16885278756648e-01 , -2.24354842925334e-03 , 9.48461220397422e-01 ) + x ( -0.31688496290754 , -0.0022435415660267 , 0.94846132594024 ) } restraint { diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index d22a51fed..74b677502 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.39806526338267e-01 , 7.75672328741349e-03 , 9.40463374035248e-01 ) ( 2.67961305267653e-03 , -1.55134465748270e-05 , -1.88092674807050e-03 ) - 1 ( -3.39400767762992e-01 , 6.96641838322646e-03 , 9.40616068253568e-01 ) ( 2.67880153552598e-03 , -1.39328367664529e-05 , -1.88123213650714e-03 ) - 2 ( -3.38846113715352e-01 , 6.28041918887901e-03 , 9.40820847746697e-01 ) ( 2.67769222743070e-03 , -1.25608383777580e-05 , -1.88164169549339e-03 ) - 3 ( -3.38130601176349e-01 , 5.70403971604277e-03 , 9.41081909548281e-01 ) ( 2.67626120235270e-03 , -1.14080794320855e-05 , -1.88216381909656e-03 ) - 4 ( -3.37247595289775e-01 , 5.23682177162826e-03 , 9.41401420845006e-01 ) ( 2.67449519057955e-03 , -1.04736435432565e-05 , -1.88280284169001e-03 ) - 5 ( -3.36197075204435e-01 , 4.87199562596542e-03 , 9.41779055980013e-01 ) ( 2.67239415040887e-03 , -9.74399125193083e-06 , -1.88355811196003e-03 ) - 6 ( -3.34986254460518e-01 , 4.59628859673558e-03 , 9.42211803923963e-01 ) ( 2.66997250892104e-03 , -9.19257719347116e-06 , -1.88442360784793e-03 ) - 7 ( -3.33629600434512e-01 , 4.39029400367674e-03 , 9.42694019834893e-01 ) ( 2.66725920086902e-03 , -8.78058800735348e-06 , -1.88538803966979e-03 ) - 8 ( -3.32148396065082e-01 , 4.22953796650038e-03 , 9.43217659927963e-01 ) ( 2.66429679213016e-03 , -8.45907593300077e-06 , -1.88643531985593e-03 ) - 9 ( -3.30569995421052e-01 , 4.08622583945091e-03 , 9.43772631985964e-01 ) ( 2.66113999084210e-03 , -8.17245167890183e-06 , -1.88754526397193e-03 ) - 10 ( -3.28926878576244e-01 , 3.93146203291304e-03 , 9.44347209534911e-01 ) ( 2.65785375715249e-03 , -7.86292406582608e-06 , -1.88869441906982e-03 ) - 11 ( -3.27255543141647e-01 , 3.73759711530038e-03 , 9.44928483987476e-01 ) ( 2.65451108628329e-03 , -7.47519423060077e-06 , -1.88985696797495e-03 ) - 12 ( -3.25595190785732e-01 , 3.48029023868332e-03 , 9.45502860554666e-01 ) ( 2.65119038157146e-03 , -6.96058047736665e-06 , -1.89100572110933e-03 ) - 13 ( -3.23986158203984e-01 , 3.13994943410309e-03 , 9.46056610362072e-01 ) ( 2.64797231640797e-03 , -6.27989886820618e-06 , -1.89211322072414e-03 ) - 14 ( -3.22468065560872e-01 , 2.70233964471342e-03 , 9.46576486108689e-01 ) ( 2.64493613112174e-03 , -5.40467928942684e-06 , -1.89315297221738e-03 ) - 15 ( -3.21077745744901e-01 , 2.15834764454486e-03 , 9.47050380245327e-01 ) ( 2.64215549148980e-03 , -4.31669528908973e-06 , -1.89410076049065e-03 ) - 16 ( -3.19847104732991e-01 , 1.50308299020222e-03 , 9.47467978527743e-01 ) ( 2.63969420946598e-03 , -3.00616598040443e-06 , -1.89493595705549e-03 ) - 17 ( -3.18801101785595e-01 , 7.34660956178514e-04 , 9.47821353301122e-01 ) ( 2.63760220357119e-03 , -1.46932191235703e-06 , -1.89564270660224e-03 ) - 18 ( -3.17956083756913e-01 , -1.46925162835371e-04 , 9.48105430432167e-01 ) ( 2.63591216751383e-03 , 2.93850325670741e-07 , -1.89621086086433e-03 ) - 19 ( -3.17318659715970e-01 , -1.14046859994299e-03 , 9.48318283872790e-01 ) ( 2.63463731943194e-03 , 2.28093719988598e-06 , -1.89663656774558e-03 ) - 20 ( -3.16885278756648e-01 , -2.24354842925334e-03 , 9.48461220397422e-01 ) ( 2.63377055751330e-03 , 4.48709685850667e-06 , -1.89692244079484e-03 ) + 0 ( -3.39806526338268e-01 , 7.75672328741356e-03 , 9.40463374035248e-01 ) ( 8.15530870605897e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 1 ( -3.39400766620267e-01 , 6.96641838972766e-03 , 9.40616068665847e-01 ) ( 8.15220403646792e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 2 ( -3.38846109203022e-01 , 6.28041922414825e-03 , 9.40820849371623e-01 ) ( 8.14796487369942e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 3 ( -3.38130591132888e-01 , 5.70403980782299e-03 , 9.41081913156339e-01 ) ( 8.14250444425201e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 4 ( -3.37247577605629e-01 , 5.23682194434203e-03 , 9.41401427179213e-01 ) ( 8.13577843358424e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 5 ( -3.36197047874025e-01 , 4.87199590719924e-03 , 9.41779065734990e-01 ) ( 8.12779457531989e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 6 ( -3.34986215606826e-01 , 4.59628901840625e-03 , 9.42211817735628e-01 ) ( 8.11861680070259e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 7 ( -3.33629548327832e-01 , 4.39029460277907e-03 , 9.42694038273218e-01 ) ( 8.10836448025633e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 8 ( -3.32148329135195e-01 , 4.22953878523764e-03 , 9.43217683493244e-01 ) ( 8.09720795287105e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 9 ( -3.30569912262612e-01 , 4.08622692462329e-03 , 9.43772661108707e-01 ) ( 8.08536164020953e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 10 ( -3.28926777947746e-01 , 3.93146343456791e-03 , 9.44347244579120e-01 ) ( 8.07307570823680e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 11 ( -3.27255423958834e-01 , 3.73759888481693e-03 , 9.44928525256858e-01 ) ( 8.06062671887748e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 12 ( -3.25595052110635e-01 , 3.48029242661170e-03 , 9.45502908301026e-01 ) ( 8.04830710826777e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 13 ( -3.23985999230891e-01 , 3.13995208813735e-03 , 9.46056664795109e-01 ) ( 8.03641324010812e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 14 ( -3.22467885600548e-01 , 2.70234280816037e-03 , 9.46576547406315e-01 ) ( 8.02523191735401e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 15 ( -3.21077544208144e-01 , 2.15835135551389e-03 , 9.47050448563694e-01 ) ( 8.01502583685384e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 16 ( -3.19846881114331e-01 , 1.50308728155497e-03 , 9.47468054010297e-01 ) ( 8.00601901893948e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 17 ( -3.18800855647703e-01 , 7.34665856107617e-04 , 9.47821436086129e-01 ) ( 7.99838342892665e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 18 ( -3.17955814716034e-01 , -1.46919629834831e-04 , 9.48105520658373e-01 ) ( 7.99222826899228e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 19 ( -3.17318367428595e-01 , -1.14046241197981e-03 , 9.48318381683039e-01 ) ( 7.98759304378998e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 20 ( -3.16884962907544e-01 , -2.24354156602667e-03 , 9.48461325940244e-01 ) ( 7.98444537125175e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 9453adc29..878956725 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,10 +1,14 @@ -colvars: Creating proxy instance 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: 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: Using LAMMPS interface, version "2020-04-07". +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available +colvars: Will read input state from file "test.colvars.state" colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -56,25 +60,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested. @@ -88,25 +92,25 @@ colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested. @@ -139,7 +143,7 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] colvars: # colvars = { one } -colvars: # zeroStepData = off [default] +colvars: # stepZeroData = off [default] colvars: # outputEnergy = off [default] colvars: # outputFreq = 10 [default] colvars: # timeStepFactor = 1 [default] @@ -149,6 +153,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -156,20 +161,19 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +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: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". -colvars: Restarting collective variable "one" from value: ( -0.316885 , -0.00224355 , 0.948461 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "one" from value: ( -0.316885 , -0.00224354 , 0.948461 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -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: 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 "rest.colvars.state". +colvars: Saving collective variables state to "test.restart.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index bdd0fbc9d..76d04dc8a 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.11217286070028e-01 , -2.42898443323087e-02 , 9.50028317637700e-01 ) + x ( -0.31121642234564 , -0.024289821938252 , 0.95002860115503 ) } restraint { diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 34cee8369..5ad213446 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.16885278925825e-01 , -2.24354838700285e-03 , 9.48461220340999e-01 ) ( 2.63377055785165e-03 , 4.48709677400570e-06 , -1.89692244068200e-03 ) - 21 ( -3.16642580904388e-01 , -3.45190420481037e-03 , 9.48538644608415e-01 ) ( 2.63328516180878e-03 , 6.90380840962073e-06 , -1.89707728921683e-03 ) - 22 ( -3.16568477880760e-01 , -4.75844630875750e-03 , 9.48557724126995e-01 ) ( 2.63313695576152e-03 , 9.51689261751500e-06 , -1.89711544825399e-03 ) - 23 ( -3.16633815018747e-01 , -6.15228914859871e-03 , 9.48527899708230e-01 ) ( 2.63326763003749e-03 , 1.23045782971974e-05 , -1.89705579941646e-03 ) - 24 ( -3.16804393259963e-01 , -7.61817772141619e-03 , 9.48460299527287e-01 ) ( 2.63360878651993e-03 , 1.52363554428324e-05 , -1.89692059905457e-03 ) - 25 ( -3.17043129341642e-01 , -9.13654504718068e-03 , 9.48367111240083e-01 ) ( 2.63408625868328e-03 , 1.82730900943614e-05 , -1.89673422248017e-03 ) - 26 ( -3.17312161322349e-01 , -1.06842583665067e-02 , 9.48260955064637e-01 ) ( 2.63462432264470e-03 , 2.13685167330134e-05 , -1.89652191012927e-03 ) - 27 ( -3.17574755104900e-01 , -1.22359324410351e-02 , 9.48154289594980e-01 ) ( 2.63514951020980e-03 , 2.44718648820701e-05 , -1.89630857918996e-03 ) - 28 ( -3.17796908059631e-01 , -1.37655526607991e-02 , 9.48058877279086e-01 ) ( 2.63559381611926e-03 , 2.75311053215982e-05 , -1.89611775455817e-03 ) - 29 ( -3.17948580714119e-01 , -1.52480894734020e-02 , 9.47985335218477e-01 ) ( 2.63589716142824e-03 , 3.04961789468039e-05 , -1.89597067043695e-03 ) - 30 ( -3.18004525582659e-01 , -1.66608199131603e-02 , 9.47942792993738e-01 ) ( 2.63600905116532e-03 , 3.33216398263206e-05 , -1.89588558598748e-03 ) - 31 ( -3.17944718562200e-01 , -1.79841856656383e-02 , 9.47938671541755e-01 ) ( 2.63588943712440e-03 , 3.59683713312766e-05 , -1.89587734308351e-03 ) - 32 ( -3.17754437600398e-01 , -1.92021681661018e-02 , 9.47978583156273e-01 ) ( 2.63550887520080e-03 , 3.84043363322036e-05 , -1.89595716631255e-03 ) - 33 ( -3.17424060652760e-01 , -2.03022834115615e-02 , 9.48066338927287e-01 ) ( 2.63484812130552e-03 , 4.06045668231230e-05 , -1.89613267785457e-03 ) - 34 ( -3.16948659679502e-01 , -2.12753545094435e-02 , 9.48204042607847e-01 ) ( 2.63389731935900e-03 , 4.25507090188870e-05 , -1.89640808521569e-03 ) - 35 ( -3.16327460461086e-01 , -2.21152123684964e-02 , 9.48392247511617e-01 ) ( 2.63265492092217e-03 , 4.42304247369928e-05 , -1.89678449502323e-03 ) - 36 ( -3.15563213187010e-01 , -2.28184431503146e-02 , 9.48630158246767e-01 ) ( 2.63112642637402e-03 , 4.56368863006293e-05 , -1.89726031649353e-03 ) - 37 ( -3.14661518372926e-01 , -2.33842572810687e-02 , 9.48915857896082e-01 ) ( 2.62932303674585e-03 , 4.67685145621374e-05 , -1.89783171579216e-03 ) - 38 ( -3.13630162181050e-01 , -2.38145070404455e-02 , 9.49246538379103e-01 ) ( 2.62726032436210e-03 , 4.76290140808910e-05 , -1.89849307675821e-03 ) - 39 ( -3.12478542660331e-01 , -2.41138300420010e-02 , 9.49618704311147e-01 ) ( 2.62495708532066e-03 , 4.82276600840020e-05 , -1.89923740862229e-03 ) - 40 ( -3.11217286070028e-01 , -2.42898443323087e-02 , 9.50028317637700e-01 ) ( 2.62243457214006e-03 , 4.85796886646174e-05 , -1.90005663527540e-03 ) + 20 ( -3.16884963116418e-01 , -2.24354151471246e-03 , 9.48461325870580e-01 ) ( 7.98444537276798e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 21 ( -3.16642241216156e-01 , -3.45189664224964e-03 , 9.48538758031100e-01 ) ( 7.98268392261178e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 ( -3.16568114024693e-01 , -4.75843803665255e-03 , 9.48557845600520e-01 ) ( 7.98214617047712e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 23 ( -3.16633426728319e-01 , -6.15228014364848e-03 , 9.48528029384117e-01 ) ( 7.98261997357673e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 ( -3.16803980244611e-01 , -7.61816796400662e-03 , 9.48460437560811e-01 ) ( 7.98385756596354e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 25 ( -3.17042691302644e-01 , -9.13653451792581e-03 , 9.48367257779695e-01 ) ( 7.98559053998928e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 ( -3.17311697949499e-01 , -1.06842470469969e-02 , 9.48261110248356e-01 ) ( 7.98754458201478e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 27 ( -3.17574266073838e-01 , -1.22359203148490e-02 , 9.48154453547370e-01 ) ( 7.98945301173086e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 ( -3.17796393029335e-01 , -1.37655397145225e-02 , 9.48059050109176e-01 ) ( 7.99106839499326e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 29 ( -3.17948039324536e-01 , -1.52480756973849e-02 , 9.47985517018699e-01 ) ( 7.99217168926526e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 ( -3.18003957452058e-01 , -1.66608053017503e-02 , 9.47942983840024e-01 ) ( 7.99257861491880e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 31 ( -3.17944123283929e-01 , -1.79841702169020e-02 , 9.47938871494794e-01 ) ( 7.99214319352307e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 ( -3.17753814739109e-01 , -1.92021518812537e-02 , 9.47978792263768e-01 ) ( 7.99075868764749e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 33 ( -3.17423409740323e-01 , -2.03022662945123e-02 , 9.48066557226935e-01 ) ( 7.98835639958574e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 ( -3.16947980211030e-01 , -2.12753365669340e-02 , 9.48204270130710e-01 ) ( 7.98490285168920e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 35 ( -3.16326751891462e-01 , -2.21151936111177e-02 , 9.48392484285562e-01 ) ( 7.98039584965398e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 ( -3.15562474928861e-01 , -2.28184235943545e-02 , 9.48630404299504e-01 ) ( 7.97485977305383e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 37 ( -3.14660749795829e-01 , -2.33842369509909e-02 , 9.48916113257725e-01 ) ( 7.96834045019333e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 ( -3.13629362612316e-01 , -2.38144859712725e-02 , 9.49246803084064e-01 ) ( 7.96090004975013e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 39 ( -3.12477711387554e-01 , -2.41138082808482e-02 , 9.49618978399332e-01 ) ( 7.95261261562472e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 ( -3.11216422345641e-01 , -2.42898219382525e-02 , 9.50028601155032e-01 ) ( 7.94356098227882e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/lammps-version.txt b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/lammps-version.txt index 308cf25eb..8b1378917 100644 --- a/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/lammps-version.txt +++ b/lammps/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/lammps-version.txt @@ -1 +1 @@ -LAMMPS (19 Mar 2020) + diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 9021512b3..d3f1df421 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,42 +1,46 @@ -colvars: Creating proxy instance 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: 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: Using LAMMPS interface, version "2019-08-17". +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 @@ -55,27 +59,27 @@ 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested. @@ -84,6 +88,8 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -99,7 +105,9 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] 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] @@ -107,6 +115,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,14 +123,14 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Writing to colvar trajectory file "test.colvars.traj". +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 final output state file will be "test.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Saving collective variables state to "test.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index 77d14316a..85310fc06 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10520638330221e-01 , 2.11605941369892e-01 , 9.26714550845056e-01 ) + x ( -0.31052032419257 , 0.21160597222382 , 0.92671464906008 ) } restraint { diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 7cf5772c5..9d3d7ff05 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.31000065675602e-01 , 2.15045616532170e-01 , 9.18800489406186e-01 ) ( 2.66200013135120e-03 , -4.30091233064339e-04 , -1.83760097881237e-03 ) - 1 ( -3.30747382610336e-01 , 2.14639350848341e-01 , 9.18986462339797e-01 ) ( 2.66149476522067e-03 , -4.29278701696682e-04 , -1.83797292467959e-03 ) - 2 ( -3.30329177496789e-01 , 2.14346254178871e-01 , 9.19205264243946e-01 ) ( 2.66065835499358e-03 , -4.28692508357742e-04 , -1.83841052848789e-03 ) - 3 ( -3.29734600584801e-01 , 2.14163956103125e-01 , 9.19461197160294e-01 ) ( 2.65946920116960e-03 , -4.28327912206250e-04 , -1.83892239432059e-03 ) - 4 ( -3.28958780020461e-01 , 2.14084704168534e-01 , 9.19757500914519e-01 ) ( 2.65791756004092e-03 , -4.28169408337068e-04 , -1.83951500182904e-03 ) - 5 ( -3.28004092876476e-01 , 2.14095348550897e-01 , 9.20095917165787e-01 ) ( 2.65600818575295e-03 , -4.28190697101795e-04 , -1.84019183433157e-03 ) - 6 ( -3.26880768658106e-01 , 2.14177647238567e-01 , 9.20476451901317e-01 ) ( 2.65376153731621e-03 , -4.28355294477135e-04 , -1.84095290380263e-03 ) - 7 ( -3.25606842414968e-01 , 2.14309070278038e-01 , 9.20897283397620e-01 ) ( 2.65121368482994e-03 , -4.28618140556076e-04 , -1.84179456679524e-03 ) - 8 ( -3.24207551977149e-01 , 2.14464183894695e-01 , 9.21354750933302e-01 ) ( 2.64841510395430e-03 , -4.28928367789389e-04 , -1.84270950186660e-03 ) - 9 ( -3.22714302509381e-01 , 2.14616523779881e-01 , 9.21843385112961e-01 ) ( 2.64542860501876e-03 , -4.29233047559763e-04 , -1.84368677022592e-03 ) - 10 ( -3.21163317452701e-01 , 2.14740685941281e-01 , 9.22355984056180e-01 ) ( 2.64232663490540e-03 , -4.29481371882561e-04 , -1.84471196811236e-03 ) - 11 ( -3.19594073699230e-01 , 2.14814254599580e-01 , 9.22883776039626e-01 ) ( 2.63918814739846e-03 , -4.29628509199160e-04 , -1.84576755207925e-03 ) - 12 ( -3.18047594360918e-01 , 2.14819200941604e-01 , 9.23416719920126e-01 ) ( 2.63609518872184e-03 , -4.29638401883208e-04 , -1.84683343984025e-03 ) - 13 ( -3.16564652603684e-01 , 2.14742518434378e-01 , 9.23943976385132e-01 ) ( 2.63312930520737e-03 , -4.29485036868756e-04 , -1.84788795277026e-03 ) - 14 ( -3.15183932269799e-01 , 2.14576058648336e-01 , 9.24454543984664e-01 ) ( 2.63036786453960e-03 , -4.29152117296673e-04 , -1.84890908796933e-03 ) - 15 ( -3.13940202629985e-01 , 2.14315723502614e-01 , 9.24938008642847e-01 ) ( 2.62788040525997e-03 , -4.28631447005229e-04 , -1.84987601728569e-03 ) - 16 ( -3.12862580359467e-01 , 2.13960296945979e-01 , 9.25385323603959e-01 ) ( 2.62572516071893e-03 , -4.27920593891957e-04 , -1.85077064720792e-03 ) - 17 ( -3.11972978093664e-01 , 2.13510244195151e-01 , 9.25789520659581e-01 ) ( 2.62394595618733e-03 , -4.27020488390303e-04 , -1.85157904131916e-03 ) - 18 ( -3.11284865571467e-01 , 2.12966776120400e-01 , 9.26146254505754e-01 ) ( 2.62256973114294e-03 , -4.25933552240800e-04 , -1.85229250901151e-03 ) - 19 ( -3.10802483758509e-01 , 2.12331386792386e-01 , 9.26454099387748e-01 ) ( 2.62160496751702e-03 , -4.24662773584772e-04 , -1.85290819877550e-03 ) - 20 ( -3.10520638330221e-01 , 2.11605941369892e-01 , 9.26714550845056e-01 ) ( 2.62104127666044e-03 , -4.23211882739785e-04 , -1.85342910169011e-03 ) + 0 ( -3.31000065675602e-01 , 2.15045616532170e-01 , 9.18800489406186e-01 ) ( 8.08858570912923e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 1 ( -3.30747381484093e-01 , 2.14639350938294e-01 , 9.18986462724127e-01 ) ( 8.08669140968446e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 2 ( -3.30329173047114e-01 , 2.14346254546632e-01 , 9.19205265757241e-01 ) ( 8.08355866805573e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 3 ( -3.29734590676862e-01 , 2.14163956938463e-01 , 9.19461200518881e-01 ) ( 8.07910997218256e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 4 ( -3.28958762569193e-01 , 2.14084705652207e-01 , 9.19757506810764e-01 ) ( 8.07331441451370e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 5 ( -3.28004065897143e-01 , 2.14095350858156e-01 , 9.20095926246751e-01 ) ( 8.06619697839623e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 6 ( -3.26880730290351e-01 , 2.14177650538226e-01 , 9.20476464758753e-01 ) ( 8.05784243783097e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 7 ( -3.25606790941200e-01 , 2.14309074731833e-01 , 9.20897300561012e-01 ) ( 8.04839404216760e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 8 ( -3.24207485834516e-01 , 2.14464189656850e-01 , 9.21354772866398e-01 ) ( 8.03804781765546e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 9 ( -3.22714220295138e-01 , 2.14616530996790e-01 , 9.21843412213921e-01 ) ( 8.02704358759226e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 10 ( -3.21163217923310e-01 , 2.14740694751249e-01 , 9.22356016661080e-01 ) ( 8.01565380093457e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 11 ( -3.19593955764015e-01 , 2.14814265132655e-01 , 9.22883814428786e-01 ) ( 8.00417108431192e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 12 ( -3.18047457071411e-01 , 2.14819213319611e-01 , 9.23416764326462e-01 ) ( 7.99289520492016e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 13 ( -3.16564495139913e-01 , 2.14742532771301e-01 , 9.23944027003681e-01 ) ( 7.98211991977728e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 14 ( -3.15183753924788e-01 , 2.14576075051174e-01 , 9.24454600982391e-01 ) ( 7.97212005497982e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 15 ( -3.13940002793540e-01 , 2.14315742072741e-01 , 9.24938072167971e-01 ) ( 7.96313916677836e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 16 ( -3.12862358502079e-01 , 2.13960317780900e-01 , 9.25385393794182e-01 ) ( 7.95537818105562e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 17 ( -3.11972733751106e-01 , 2.13510267390426e-01 , 9.25789597648802e-01 ) ( 7.94898554465525e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 18 ( -3.11284598330463e-01 , 2.12966801771410e-01 , 9.26146338429030e-01 ) ( 7.94404958673316e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 19 ( -3.10802193243697e-01 , 2.12331414995671e-01 , 9.26454190384416e-01 ) ( 7.94059389853281e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 20 ( -3.10520324192575e-01 , 2.11605972223816e-01 , 9.26714649060082e-01 ) ( 7.93857648476372e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 0435583fe..9bf705e75 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,42 +1,47 @@ -colvars: Creating proxy instance 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: 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: Using LAMMPS interface, version "2019-08-17". +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 2) +colvars: - Multiple replicas: available, but not (yet) enabled +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: not available +colvars: Will read input state from file "test.colvars.state" colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] colvars: # indexFile = "index.ndx" -colvars: The following index groups were read from the index file "index.ndx": -colvars: Protein (104 atoms). -colvars: Protein_noH (51 atoms). -colvars: Protein_Backbone (40 atoms). -colvars: Protein_C-alpha (10 atoms). -colvars: RMSD_atoms (10 atoms). -colvars: Protein_C-alpha_1_2 (2 atoms). -colvars: Protein_C-alpha_9_10 (2 atoms). -colvars: Protein_C-alpha_1 (1 atoms). -colvars: group1 (4 atoms). -colvars: Protein_C-alpha_2 (1 atoms). -colvars: group2 (4 atoms). -colvars: Protein_C-alpha_3 (1 atoms). -colvars: group3 (4 atoms). -colvars: Protein_C-alpha_4 (1 atoms). -colvars: group4 (4 atoms). -colvars: Protein_C-alpha_5 (1 atoms). -colvars: group5 (4 atoms). -colvars: Protein_C-alpha_6 (1 atoms). -colvars: group6 (4 atoms). -colvars: Protein_C-alpha_7 (1 atoms). -colvars: group7 (4 atoms). -colvars: Protein_C-alpha_8 (1 atoms). -colvars: group8 (4 atoms). -colvars: Protein_C-alpha_9 (1 atoms). -colvars: group9 (4 atoms). -colvars: Protein_C-alpha_10 (1 atoms). -colvars: group10 (4 atoms). -colvars: heavy_atoms (51 atoms). +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 @@ -55,27 +60,27 @@ 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "group2" defined with 4 atoms requested. @@ -84,6 +89,8 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: # timeStepFactor = 1 [default] colvars: # width = 0.5 +colvars: # hardLowerBoundary = off [default] +colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] @@ -99,7 +106,9 @@ colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. colvars: # name = "harmonic1" [default] 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] @@ -107,6 +116,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -114,18 +124,19 @@ colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +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: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". -colvars: Restarting collective variable "one" from value: ( -0.310521 , 0.211606 , 0.926715 ) +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "one" from value: ( -0.31052 , 0.211606 , 0.926715 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "rest.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Writing to colvar trajectory file "test.restart.colvars.traj". -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: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". -colvars: Saving collective variables state to "rest.colvars.state". colvars: Saving collective variables state to "test.restart.colvars.state". -colvars: Resetting the Collective Variables module. +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.colvars.state". +colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 96617ed46..b328cf6a2 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08081780755740e-01 , 1.95871163616261e-01 , 9.30978036062068e-01 ) + x ( -0.30808091021275 , 0.19587126091261 , 0.93097830367361 ) } restraint { diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index f7de85949..73fcad266 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10520638498220e-01 , 2.11605941407779e-01 , 9.26714550780112e-01 ) ( 2.62104127699644e-03 , -4.23211882815559e-04 , -1.85342910156022e-03 ) - 21 ( -3.10425143807960e-01 , 2.10793243179139e-01 , 9.26931733582267e-01 ) ( 2.62085028761592e-03 , -4.21586486358278e-04 , -1.85386346716453e-03 ) - 22 ( -3.10493900986171e-01 , 2.09897877002036e-01 , 9.27111869560749e-01 ) ( 2.62098780197234e-03 , -4.19795754004073e-04 , -1.85422373912150e-03 ) - 23 ( -3.10698494668286e-01 , 2.08927049839855e-01 , 9.27262602101516e-01 ) ( 2.62139698933657e-03 , -4.17854099679711e-04 , -1.85452520420303e-03 ) - 24 ( -3.11006118352854e-01 , 2.07891155834252e-01 , 9.27392291143823e-01 ) ( 2.62201223670571e-03 , -4.15782311668505e-04 , -1.85478458228765e-03 ) - 25 ( -3.11381607950602e-01 , 2.06803879538600e-01 , 9.27509379811267e-01 ) ( 2.62276321590120e-03 , -4.13607759077200e-04 , -1.85501875962253e-03 ) - 26 ( -3.11789377198737e-01 , 2.05681790110946e-01 , 9.27621897910340e-01 ) ( 2.62357875439747e-03 , -4.11363580221891e-04 , -1.85524379582068e-03 ) - 27 ( -3.12195094558641e-01 , 2.04543518350666e-01 , 9.27737124423860e-01 ) ( 2.62439018911728e-03 , -4.09087036701332e-04 , -1.85547424884772e-03 ) - 28 ( -3.12567002967105e-01 , 2.03408712495852e-01 , 9.27861392847521e-01 ) ( 2.62513400593421e-03 , -4.06817424991704e-04 , -1.85572278569504e-03 ) - 29 ( -3.12876847101832e-01 , 2.02297009505196e-01 , 9.27999999187970e-01 ) ( 2.62575369420366e-03 , -4.04594019010392e-04 , -1.85599999837594e-03 ) - 30 ( -3.13100427083966e-01 , 2.01227224817514e-01 , 9.28157166945383e-01 ) ( 2.62620085416793e-03 , -4.02454449635027e-04 , -1.85631433389077e-03 ) - 31 ( -3.13217827312105e-01 , 2.00216869203902e-01 , 9.28336037187005e-01 ) ( 2.62643565462421e-03 , -4.00433738407804e-04 , -1.85667207437401e-03 ) - 32 ( -3.13213385314631e-01 , 1.99281971542051e-01 , 9.28538675057782e-01 ) ( 2.62642677062926e-03 , -3.98563943084103e-04 , -1.85707735011556e-03 ) - 33 ( -3.13075470992557e-01 , 1.98437074527069e-01 , 9.28766104525745e-01 ) ( 2.62615094198511e-03 , -3.96874149054139e-04 , -1.85753220905149e-03 ) - 34 ( -3.12796145444057e-01 , 1.97695222914567e-01 , 9.29018390685620e-01 ) ( 2.62559229088811e-03 , -3.95390445829134e-04 , -1.85803678137124e-03 ) - 35 ( -3.12370771656743e-01 , 1.97067798459528e-01 , 9.29294777680842e-01 ) ( 2.62474154331349e-03 , -3.94135596919056e-04 , -1.85858955536168e-03 ) - 36 ( -3.11797637855373e-01 , 1.96564141853387e-01 , 9.29593874315688e-01 ) ( 2.62359527571075e-03 , -3.93128283706774e-04 , -1.85918774863138e-03 ) - 37 ( -3.11077651580314e-01 , 1.96191001516941e-01 , 9.29913859242380e-01 ) ( 2.62215530316063e-03 , -3.92382003033881e-04 , -1.85982771848476e-03 ) - 38 ( -3.10214144759863e-01 , 1.95951922717104e-01 , 9.30252669103603e-01 ) ( 2.62042828951973e-03 , -3.91903845434209e-04 , -1.86050533820721e-03 ) - 39 ( -3.09212811759702e-01 , 1.95846719625682e-01 , 9.30608134208765e-01 ) ( 2.61842562351940e-03 , -3.91693439251365e-04 , -1.86121626841753e-03 ) - 40 ( -3.08081780755740e-01 , 1.95871163616261e-01 , 9.30978036062068e-01 ) ( 2.61616356151148e-03 , -3.91742327232521e-04 , -1.86195607212414e-03 ) + 20 ( -3.10520324398850e-01 , 2.11605972269678e-01 , 9.26714648980492e-01 ) ( 7.93857648623961e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 21 ( -3.10424805734108e-01 , 2.10793276787821e-01 , 9.26931839158627e-01 ) ( 7.93789312444490e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 ( -3.10493538612485e-01 , 2.09897913458412e-01 , 9.27111982667521e-01 ) ( 7.93838483988443e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 23 ( -3.10698107690827e-01 , 2.08927089247761e-01 , 9.27262722886991e-01 ) ( 7.93984878018462e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 ( -3.11005706444300e-01 , 2.07891198291710e-01 , 9.27392419761947e-01 ) ( 7.94205129710450e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 25 ( -3.11381170775917e-01 , 2.06803925138841e-01 , 9.27509516411227e-01 ) ( 7.94474183221645e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 ( -3.11788914412186e-01 , 2.05681838939914e-01 , 9.27622042633726e-01 ) ( 7.94766626618282e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 27 ( -3.12194605801322e-01 , 2.04543570484610e-01 , 9.27737277402371e-01 ) ( 7.95057866023351e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 ( -3.12566487864455e-01 , 2.03408767999376e-01 , 9.27861554201410e-01 ) ( 7.95325069364885e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 29 ( -3.12876305261082e-01 , 2.02297068430090e-01 , 9.28000169025182e-01 ) ( 7.95547850182954e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 ( -3.13099858091137e-01 , 2.01227287202652e-01 , 9.28157345361427e-01 ) ( 7.95708697807949e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 31 ( -3.13217230728332e-01 , 2.00216935076192e-01 , 9.28336224265525e-01 ) ( 7.95793180778000e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 ( -3.13212760671947e-01 , 1.99282040918217e-01 , 9.28538870871719e-01 ) ( 7.95789962890178e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 33 ( -3.13074817789498e-01 , 1.98437147415817e-01 , 9.28766309138928e-01 ) ( 7.95690677104048e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 ( -3.12795463141561e-01 , 1.97695299318581e-01 , 9.29018604154617e-01 ) ( 7.95489703847720e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 35 ( -3.12370059674796e-01 , 1.97067878376849e-01 , 9.29295000056931e-01 ) ( 7.95183904457534e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 ( -3.11796895571320e-01 , 1.96564225277970e-01 , 9.29594105646630e-01 ) ( 7.94772353587240e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 37 ( -3.11076878328621e-01 , 1.96191088438347e-01 , 9.29914099574093e-01 ) ( 7.94256113138845e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 ( -3.10213339833623e-01 , 1.95952013119794e-01 , 9.30252918481619e-01 ) ( 7.93638077465368e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 39 ( -3.09211974413949e-01 , 1.95846813488462e-01 , 9.30608392679457e-01 ) ( 7.92922906034774e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 ( -3.08080910212750e-01 , 1.95871260912607e-01 , 9.30978303673608e-01 ) ( 7.92117043673167e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/lammps-version.txt b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/lammps-version.txt index 646d758cf..8b1378917 100644 --- a/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/lammps-version.txt +++ b/lammps/tests/library/000_distancedir_harmonic-ddir-fixed/lammps-version.txt @@ -1 +1 @@ -LAMMPS (12 Dec 2018) + diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out index abb32eebd..28b398a86 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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] @@ -42,6 +49,7 @@ 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" @@ -55,25 +63,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +95,25 @@ 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 = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +156,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,19 +167,33 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 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: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +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 (51 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 = 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". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index f4d2ca8a0..e0397b4c7 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) + x ( -0.3172743324774 , -0.0018905287033722 , 0.94833191649983 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 653638305..7a9c4369f 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.39806527406457e-01 , 7.75672148823417e-03 , 9.40463373664131e-01 ) ( 2.67961305481292e-03 , -1.55134429764683e-05 , -1.88092674732826e-03 ) - 1 ( -3.39402299531197e-01 , 6.96783241200742e-03 , 9.40615505073361e-01 ) ( 2.67880459906239e-03 , -1.39356648240148e-05 , -1.88123101014672e-03 ) - 2 ( -3.38852268623157e-01 , 6.28615128581265e-03 , 9.40818592689872e-01 ) ( 2.67770453724631e-03 , -1.25723025716253e-05 , -1.88163718537974e-03 ) - 3 ( -3.38144430394757e-01 , 5.71702991439356e-03 , 9.41076861771643e-01 ) ( 2.67628886078951e-03 , -1.14340598287871e-05 , -1.88215372354329e-03 ) - 4 ( -3.37272058710501e-01 , 5.26001267291420e-03 , 9.41392527418750e-01 ) ( 2.67454411742100e-03 , -1.05200253458284e-05 , -1.88278505483750e-03 ) - 5 ( -3.36235002718839e-01 , 4.90828500862304e-03 , 9.41765327289626e-01 ) ( 2.67247000543768e-03 , -9.81657001724609e-06 , -1.88353065457925e-03 ) - 6 ( -3.35040319485078e-01 , 4.64847236523130e-03 , 9.42192324328747e-01 ) ( 2.67008063897016e-03 , -9.29694473046260e-06 , -1.88438464865749e-03 ) - 7 ( -3.33702304368059e-01 , 4.46100232057914e-03 , 9.42667954010182e-01 ) ( 2.66740460873612e-03 , -8.92200464115828e-06 , -1.88533590802036e-03 ) - 8 ( -3.32242055295591e-01 , 4.32116578267109e-03 , 9.43184257830484e-01 ) ( 2.66448411059118e-03 , -8.64233156534219e-06 , -1.88636851566097e-03 ) - 9 ( -3.30686722614415e-01 , 4.20085972373069e-03 , 9.43731235185166e-01 ) ( 2.66137344522883e-03 , -8.40171944746138e-06 , -1.88746247037033e-03 ) - 10 ( -3.29068550340716e-01 , 4.07080426330041e-03 , 9.44297261316218e-01 ) ( 2.65813710068143e-03 , -8.14160852660083e-06 , -1.88859452263244e-03 ) - 11 ( -3.27423742891617e-01 , 3.90288350488177e-03 , 9.44869546599525e-01 ) ( 2.65484748578323e-03 , -7.80576700976354e-06 , -1.88973909319905e-03 ) - 12 ( -3.25791132271727e-01 , 3.67221266789039e-03 , 9.45434637078221e-01 ) ( 2.65158226454345e-03 , -7.34442533578077e-06 , -1.89086927415644e-03 ) - 13 ( -3.24210587689955e-01 , 3.35858640100320e-03 , 9.45978971609370e-01 ) ( 2.64842117537991e-03 , -6.71717280200640e-06 , -1.89195794321874e-03 ) - 14 ( -3.22721152712020e-01 , 2.94710470864841e-03 , 9.46489499237081e-01 ) ( 2.64544230542404e-03 , -5.89420941729682e-06 , -1.89297899847416e-03 ) - 15 ( -3.21358984421525e-01 , 2.42796438390647e-03 , 9.46954332647840e-01 ) ( 2.64271796884305e-03 , -4.85592876781293e-06 , -1.89390866529568e-03 ) - 16 ( -3.20155244264332e-01 , 1.79559468838712e-03 , 9.47363391423672e-01 ) ( 2.64031048852866e-03 , -3.59118937677423e-06 , -1.89472678284734e-03 ) - 17 ( -3.19134137515970e-01 , 1.04747307744542e-03 , 9.47708976992457e-01 ) ( 2.63826827503194e-03 , -2.09494615489084e-06 , -1.89541795398491e-03 ) - 18 ( -3.18311310856538e-01 , 1.83029974893031e-04 , 9.47986221355997e-01 ) ( 2.63662262171308e-03 , -3.66059949786063e-07 , -1.89597244271199e-03 ) - 19 ( -3.17692796906620e-01 , -7.96993701676326e-04 , 9.48193361922919e-01 ) ( 2.63538559381324e-03 , 1.59398740335265e-06 , -1.89638672384584e-03 ) - 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) + 0 ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ) ( 8.15530871423613e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 1 ( -3.39402298411440e-01 , 6.96783242334041e-03 , 9.40615505477319e-01 ) ( 8.15221575138462e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 2 ( -3.38852264154975e-01 , 6.28615133078170e-03 , 9.40818594298866e-01 ) ( 8.14801188470102e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 3 ( -3.38144420391855e-01 , 5.71703001573073e-03 , 9.41076865365235e-01 ) ( 8.14260989427831e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 4 ( -3.37272041061004e-01 , 5.26001285515798e-03 , 9.41392533741005e-01 ) ( 8.13596458655875e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 5 ( -3.36234975414387e-01 , 4.90828529948865e-03 , 9.41765337036518e-01 ) ( 8.12808247638885e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 6 ( -3.35040280645373e-01 , 4.64847279677808e-03 , 9.42192338137881e-01 ) ( 8.11902604400633e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 7 ( -3.33702252259637e-01 , 4.46100292996774e-03 , 9.42667972453559e-01 ) ( 8.10891307913864e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 8 ( -3.32241988344030e-01 , 4.32116661230445e-03 , 9.43184281410751e-01 ) ( 8.09791225217468e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 9 ( -3.30686639409774e-01 , 4.20086082066063e-03 , 9.43731264335476e-01 ) ( 8.08623621008283e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 10 ( -3.29068449636567e-01 , 4.07080567789454e-03 , 9.44297296403479e-01 ) ( 8.07413316093098e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 11 ( -3.27423623598501e-01 , 3.90288528891015e-03 , 9.44869587930551e-01 ) ( 8.06187736521308e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 12 ( -3.25790993446301e-01 , 3.67221487238642e-03 , 9.45434684908060e-01 ) ( 8.04975849361570e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 13 ( -3.24210428520897e-01 , 3.35858907422145e-03 , 9.45979026151070e-01 ) ( 8.03806954037997e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 14 ( -3.22720972504239e-01 , 2.94710789451937e-03 , 9.46489560671947e-01 ) ( 8.02709326120616e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 15 ( -3.21358782579701e-01 , 2.42796812120475e-03 , 9.46954401135395e-01 ) ( 8.01708769692019e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 16 ( -3.20155020276626e-01 , 1.79559901066839e-03 , 9.47363467110626e-01 ) ( 8.00827180552566e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 17 ( -3.19133890938405e-01 , 1.04747801361630e-03 , 9.47709060020176e-01 ) ( 8.00081247853456e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 18 ( -3.18311041298441e-01 , 1.83035550177083e-04 , 9.47986311866099e-01 ) ( 7.99481424229644e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 19 ( -3.17692504017315e-01 , -7.96987464681055e-04 , 9.48193460060862e-01 ) ( 7.99031277660152e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 20 ( -3.17274332477398e-01 , -1.89052870337220e-03 , 9.48331916499832e-01 ) ( 7.98727309062078e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 9097222e0..8fedac487 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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] @@ -42,6 +49,7 @@ 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" @@ -55,25 +63,25 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group1": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -87,25 +95,25 @@ 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 = on -colvars: # rotateReference = on +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = on +colvars: # rotateToReference = on colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: Within atom group "group2": colvars: Initializing atom group "fittingGroup". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "heavy_atoms" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: # printAtomIDs = off [default] colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. @@ -148,6 +156,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -158,24 +167,38 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (51 atoms). colvars: updating group data (0 scalable groups, 0 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: 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: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". -colvars: Restarting collective variable "one" from value: ( -0.317275 , -0.00189054 , 0.948332 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "one" from value: ( -0.317274 , -0.00189053 , 0.948332 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -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: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (51 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 = 0 K). +colvars: Current simulation parameters: initial step = 20, 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.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.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". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index f3e20f202..2811d5c2d 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) + x ( -0.31159739595432 , -0.024459037539329 , 0.94989937273226 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 7d738d1c8..c8c5aa686 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.17274649020541e-01 , -1.89053562305431e-03 , 9.48331810583169e-01 ) ( 2.63454929804108e-03 , 3.78107124610862e-06 , -1.89666362116634e-03 ) - 21 ( -3.17043326283096e-01 , -3.09358622124357e-03 , 9.48406009567444e-01 ) ( 2.63408665256619e-03 , 6.18717244248714e-06 , -1.89681201913489e-03 ) - 22 ( -3.16976780479176e-01 , -4.39920685529361e-03 , 9.48423095256595e-01 ) ( 2.63395356095835e-03 , 8.79841371058722e-06 , -1.89684619051319e-03 ) - 23 ( -3.17046097666149e-01 , -5.79657340749948e-03 , 9.48392414399967e-01 ) ( 2.63409219533230e-03 , 1.15931468149990e-05 , -1.89678482879993e-03 ) - 24 ( -3.17217482859608e-01 , -7.27041162129638e-03 , 9.48324949415057e-01 ) ( 2.63443496571922e-03 , 1.45408232425928e-05 , -1.89664989883011e-03 ) - 25 ( -3.17454369154660e-01 , -8.80106277336966e-03 , 9.48232706037224e-01 ) ( 2.63490873830932e-03 , 1.76021255467393e-05 , -1.89646541207445e-03 ) - 26 ( -3.17719471466479e-01 , -1.03652349405030e-02 , 9.48128102819281e-01 ) ( 2.63543894293296e-03 , 2.07304698810060e-05 , -1.89625620563856e-03 ) - 27 ( -3.17976646119255e-01 , -1.19373246135143e-02 , 9.48023392540407e-01 ) ( 2.63595329223851e-03 , 2.38746492270286e-05 , -1.89604678508081e-03 ) - 28 ( -3.18192455781236e-01 , -1.34910475011762e-02 , 9.47930141266342e-01 ) ( 2.63638491156247e-03 , 2.69820950023524e-05 , -1.89586028253268e-03 ) - 29 ( -3.18337378885354e-01 , -1.50010625401725e-02 , 9.47858787650918e-01 ) ( 2.63667475777071e-03 , 3.00021250803450e-05 , -1.89571757530184e-03 ) - 30 ( -3.18386627833720e-01 , -1.64443011529380e-02 , 9.47818305465907e-01 ) ( 2.63677325566744e-03 , 3.28886023058761e-05 , -1.89563661093181e-03 ) - 31 ( -3.18320580791560e-01 , -1.78008340545886e-02 , 9.47815983274963e-01 ) ( 2.63664116158312e-03 , 3.56016681091771e-05 , -1.89563196654993e-03 ) - 32 ( -3.18124861601468e-01 , -1.90542515702588e-02 , 9.47857324668720e-01 ) ( 2.63624972320294e-03 , 3.81085031405176e-05 , -1.89571464933744e-03 ) - 33 ( -3.17790139900921e-01 , -2.01916660122652e-02 , 9.47946055219073e-01 ) ( 2.63558027980184e-03 , 4.03833320245304e-05 , -1.89589211043815e-03 ) - 34 ( -3.17311724965833e-01 , -2.12034927401992e-02 , 9.48084216246017e-01 ) ( 2.63462344993167e-03 , 4.24069854803984e-05 , -1.89616843249203e-03 ) - 35 ( -3.16689033052138e-01 , -2.20831582105308e-02 , 9.48272318729146e-01 ) ( 2.63337806610428e-03 , 4.41663164210616e-05 , -1.89654463745829e-03 ) - 36 ( -3.15924962100982e-01 , -2.28268525064398e-02 , 9.48509542981062e-01 ) ( 2.63184992420196e-03 , 4.56537050128795e-05 , -1.89701908596212e-03 ) - 37 ( -3.15025224091246e-01 , -2.34334009818228e-02 , 9.48793962831070e-01 ) ( 2.63005044818249e-03 , 4.68668019636457e-05 , -1.89758792566214e-03 ) - 38 ( -3.13997688281053e-01 , -2.39042792438929e-02 , 9.49122772452534e-01 ) ( 2.62799537656211e-03 , 4.78085584877859e-05 , -1.89824554490507e-03 ) - 39 ( -3.12851813200530e-01 , -2.42437511657998e-02 , 9.49492487335498e-01 ) ( 2.62570362640106e-03 , 4.84875023315996e-05 , -1.89898497467100e-03 ) - 40 ( -3.11598263889815e-01 , -2.44590603702029e-02 , 9.49899087433323e-01 ) ( 2.62319652777963e-03 , 4.89181207404057e-05 , -1.89979817486665e-03 ) + 20 ( -3.17274332477398e-01 , -1.89052870337220e-03 , 9.48331916499832e-01 ) ( 7.98727309062078e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 21 ( -3.17042985781091e-01 , -3.09357859873036e-03 , 9.48406123418899e-01 ) ( 7.98559267840108e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 ( -3.16976415722013e-01 , -4.39919851009075e-03 , 9.48423217202370e-01 ) ( 7.98510930365351e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 23 ( -3.17045708359206e-01 , -5.79656431974707e-03 , 9.48392544600123e-01 ) ( 7.98561244899291e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 ( -3.17217068704307e-01 , -7.27040177116643e-03 , 9.48325088026639e-01 ) ( 7.98685706633039e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 25 ( -3.17453929844126e-01 , -8.80105214138750e-03 , 9.48232853210500e-01 ) ( 7.98857822734492e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 ( -3.17719006682163e-01 , -1.03652235082699e-02 , 9.48128258694214e-01 ) ( 7.99050552203427e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 27 ( -3.17976155528276e-01 , -1.19373123646175e-02 , 9.48023557243683e-01 ) ( 7.99237628913269e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 ( -3.18191939033572e-01 , -1.34910344220521e-02 , 9.47930314909423e-01 ) ( 7.99394696958977e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 29 ( -3.18336835611903e-01 , -1.50010486207664e-02 , 9.47858970328855e-01 ) ( 7.99500210107567e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 ( -3.18386057643919e-01 , -1.64442863867876e-02 , 9.47818497257356e-01 ) ( 7.99536061354955e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 31 ( -3.18319983270215e-01 , -1.78008184384029e-02 , 9.47816184243429e-01 ) ( 7.99487936500546e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 ( -3.18124236305012e-01 , -1.90542351033151e-02 , 9.47857534864803e-01 ) ( 7.99345408051785e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 33 ( -3.17789486353393e-01 , -2.01916486958893e-02 , 9.47946274683428e-01 ) ( 7.99101815494508e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 ( -3.17311042655102e-01 , -2.12034745779205e-02 , 9.48084445012656e-01 ) ( 7.98753982055380e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 35 ( -3.16688321426000e-01 , -2.20831392092381e-02 , 9.48272556829021e-01 ) ( 7.98301825505653e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 ( -3.15924220565715e-01 , -2.28268326781806e-02 , 9.48509790444900e-01 ) ( 7.97747889430861e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 37 ( -3.15024452010716e-01 , -2.34333803463575e-02 , 9.48794219691968e-01 ) ( 7.97096834859700e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 ( -3.13996884977412e-01 , -2.39042578311307e-02 , 9.49123038747888e-01 ) ( 7.96354934872890e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 39 ( -3.12850977956734e-01 , -2.42437290173447e-02 , 9.49492763108202e-01 ) ( 7.95529632172554e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 ( -3.11597395954319e-01 , -2.44590375393289e-02 , 9.49899372732258e-01 ) ( 7.94629231445762e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt index 129300d44..1b9427efe 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.13 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2018-11-16. -colvars: Using NAMD interface, version 2018-08-29. +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-10-05. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out index 1d23f8568..664194c57 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out @@ -1,9 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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] @@ -42,6 +49,7 @@ 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" @@ -55,28 +63,28 @@ 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: # 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: # 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +121,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,19 +132,33 @@ 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: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped index e64cb9b15..89627fa18 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) + x ( -0.31090111744619 , 0.2119045651289 , 0.92651872644229 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj index 8935a8e9e..b7c68e9db 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 0 ( -3.31000066838100e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223397e-04 , -1.83760097863971e-03 ) - 1 ( -3.30748902386919e-01 , 2.14640582516973e-01 , 9.18985627693177e-01 ) ( 2.66149780477384e-03 , -4.29281165033946e-04 , -1.83797125538635e-03 ) - 2 ( -3.30335278614263e-01 , 2.14351255518651e-01 , 9.19201905437763e-01 ) ( 2.66067055722853e-03 , -4.28702511037302e-04 , -1.83840381087553e-03 ) - 3 ( -3.29748301598012e-01 , 2.14175295385314e-01 , 9.19453642354981e-01 ) ( 2.65949660319602e-03 , -4.28350590770628e-04 , -1.83890728470996e-03 ) - 4 ( -3.28983003286818e-01 , 2.14104941848711e-01 , 9.19744126061344e-01 ) ( 2.65796600657364e-03 , -4.28209883697422e-04 , -1.83948825212269e-03 ) - 5 ( -3.28041624986510e-01 , 2.14126988066820e-01 , 9.20075173699216e-01 ) ( 2.65608324997302e-03 , -4.28253976133641e-04 , -1.84015034739843e-03 ) - 6 ( -3.26934234947895e-01 , 2.14223081728789e-01 , 9.20446889979892e-01 ) ( 2.65386846989579e-03 , -4.28446163457579e-04 , -1.84089377995978e-03 ) - 7 ( -3.25678693151725e-01 , 2.14370527632503e-01 , 9.20857570805359e-01 ) ( 2.65135738630345e-03 , -4.28741055265006e-04 , -1.84171514161072e-03 ) - 8 ( -3.24300051451023e-01 , 2.14543670052469e-01 , 9.21303690576175e-01 ) ( 2.64860010290205e-03 , -4.29087340104938e-04 , -1.84260738115235e-03 ) - 9 ( -3.22829511499202e-01 , 2.14715764651319e-01 , 9.21779934103247e-01 ) ( 2.64565902299840e-03 , -4.29431529302638e-04 , -1.84355986820649e-03 ) - 10 ( -3.21303059779930e-01 , 2.14861065895251e-01 , 9.22279277734468e-01 ) ( 2.64260611955986e-03 , -4.29722131790503e-04 , -1.84455855546894e-03 ) - 11 ( -3.19759879034225e-01 , 2.14956751273127e-01 , 9.22793159295257e-01 ) ( 2.63951975806845e-03 , -4.29913502546255e-04 , -1.84558631859051e-03 ) - 12 ( -3.18240618894718e-01 , 2.14984320891132e-01 , 9.23311783882609e-01 ) ( 2.63648123778944e-03 , -4.29968641782263e-04 , -1.84662356776522e-03 ) - 13 ( -3.16785580628539e-01 , 2.14930240610141e-01 , 9.23824597841553e-01 ) ( 2.63357116125708e-03 , -4.29860481220281e-04 , -1.84764919568311e-03 ) - 14 ( -3.15432869486022e-01 , 2.14785792588681e-01 , 9.24320922704807e-01 ) ( 2.63086573897204e-03 , -4.29571585177362e-04 , -1.84864184540961e-03 ) - 15 ( -3.14216581896700e-01 , 2.14546290781891e-01 , 9.24790694575203e-01 ) ( 2.62843316379340e-03 , -4.29092581563783e-04 , -1.84958138915041e-03 ) - 16 ( -3.13165103302749e-01 , 2.14209940590278e-01 , 9.25225226323671e-01 ) ( 2.62633020660550e-03 , -4.28419881180556e-04 , -1.85045045264734e-03 ) - 17 ( -3.12299612195620e-01 , 2.13776666349982e-01 , 9.25617895865650e-01 ) ( 2.62459922439124e-03 , -4.27553332699964e-04 , -1.85123579173130e-03 ) - 18 ( -3.11632909053414e-01 , 2.13247200164350e-01 , 9.25964665425724e-01 ) ( 2.62326581810683e-03 , -4.26494400328700e-04 , -1.85192933085145e-03 ) - 19 ( -3.11168697605864e-01 , 2.12622637201006e-01 , 9.26264355235566e-01 ) ( 2.62233739521173e-03 , -4.25245274402012e-04 , -1.85252871047113e-03 ) - 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) + 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 8.08858571784670e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 1 ( -3.30748901282821e-01 , 2.14640582611379e-01 , 9.18985628068499e-01 ) ( 8.08670279984310e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 2 ( -3.30335274160198e-01 , 2.14351255887462e-01 , 9.19201906952425e-01 ) ( 8.08360434876203e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 3 ( -3.29748291719458e-01 , 2.14175296229649e-01 , 9.19453645701099e-01 ) ( 8.07921241494130e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 4 ( -3.28982985836416e-01 , 2.14104943336954e-01 , 9.19744131956729e-01 ) ( 8.07349520836485e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 5 ( -3.28041598033954e-01 , 2.14126990387345e-01 , 9.20075182768771e-01 ) ( 8.06647648998534e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 6 ( -3.26934196597747e-01 , 2.14223085043033e-01 , 9.20446902830159e-01 ) ( 8.05823958872875e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 7 ( -3.25678641682616e-01 , 2.14370532102599e-01 , 9.20857587967768e-01 ) ( 8.04892619635360e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 8 ( -3.24299985295791e-01 , 2.14543675833100e-01 , 9.21303712516764e-01 ) ( 8.03873071326494e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 9 ( -3.22829429250180e-01 , 2.14715771889361e-01 , 9.21779961222829e-01 ) ( 8.02789124478707e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 10 ( -3.21302960188206e-01 , 2.14861074729567e-01 , 9.22279310372054e-01 ) ( 8.01667833699727e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 11 ( -3.19759761003375e-01 , 2.14956761834407e-01 , 9.22793197734319e-01 ) ( 8.00538237726394e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 12 ( -3.18240481470294e-01 , 2.14984333301966e-01 , 9.23311828359338e-01 ) ( 7.99430041491093e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 13 ( -3.16785422984341e-01 , 2.14930254985405e-01 , 9.23824648554335e-01 ) ( 7.98372288505808e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 14 ( -3.15432690908641e-01 , 2.14785809036403e-01 , 9.24320979823953e-01 ) ( 7.97392063237946e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 15 ( -3.14216381769318e-01 , 2.14546309404606e-01 , 9.24790758252190e-01 ) ( 7.96513265420902e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 16 ( -3.13164881089158e-01 , 2.14209961486685e-01 , 9.25225296699289e-01 ) ( 7.95755497557056e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 17 ( -3.12299367429557e-01 , 2.13776689609900e-01 , 9.25617973076653e-01 ) ( 7.95133116198311e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 18 ( -3.11632641304657e-01 , 2.13247225899134e-01 , 9.25964749609728e-01 ) ( 7.94654511959021e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 19 ( -3.11168406491660e-01 , 2.12622665501026e-01 , 9.26264446536020e-01 ) ( 7.94321690689054e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 20 ( -3.10901117446188e-01 , 2.11904565128898e-01 , 9.26518726442291e-01 ) ( 7.94130223072518e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out index 42c1974d9..d4fbfba3d 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.out @@ -1,9 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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] @@ -42,6 +49,7 @@ 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" @@ -55,28 +63,28 @@ 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: # 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: # 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -113,6 +121,7 @@ colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( 1 , 0 , 0 ) } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -123,24 +132,38 @@ 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: 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: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from text file "test.colvars.state". colvars: Restarting collective variable "one" from value: ( -0.310901 , 0.211905 , 0.926519 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -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: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. 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 = 20, 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.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.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". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped index 6b8d538b6..dcb77c75f 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) + x ( -0.30847734451325 , 0.19566215305744 , 0.93089099779887 ) } restraint { diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj index 0b3f5ab28..2090cb4fc 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 ( -3.10901432271994e-01 , 2.11904534162306e-01 , 9.26518627882181e-01 ) ( 2.62180286454399e-03 , -4.23809068324612e-04 , -1.85303725576436e-03 ) - 21 ( -3.10816792220306e-01 , 2.11095479027854e-01 , 9.26731687387390e-01 ) ( 2.62163358444061e-03 , -4.22190958055708e-04 , -1.85346337477478e-03 ) - 22 ( -3.10892759748286e-01 , 2.10199933231990e-01 , 9.26909747497221e-01 ) ( 2.62178551949657e-03 , -4.20399866463979e-04 , -1.85381949499444e-03 ) - 23 ( -3.11101193207355e-01 , 2.09225066830326e-01 , 9.27060364266969e-01 ) ( 2.62220238641471e-03 , -4.18450133660652e-04 , -1.85412072853394e-03 ) - 24 ( -3.11409711041452e-01 , 2.08181314903498e-01 , 9.27191744998913e-01 ) ( 2.62281942208290e-03 , -4.16362629806997e-04 , -1.85438348999783e-03 ) - 25 ( -3.11783673453337e-01 , 2.07082466730478e-01 , 9.27312133502395e-01 ) ( 2.62356734690667e-03 , -4.14164933460955e-04 , -1.85462426700479e-03 ) - 26 ( -3.12188067442232e-01 , 2.05945244407307e-01 , 9.27429332538441e-01 ) ( 2.62437613488447e-03 , -4.11890488814613e-04 , -1.85485866507688e-03 ) - 27 ( -3.12589140366756e-01 , 2.04788460697038e-01 , 9.27550384448258e-01 ) ( 2.62517828073351e-03 , -4.09576921394075e-04 , -1.85510076889652e-03 ) - 28 ( -3.12955685129617e-01 , 2.03631959627123e-01 , 9.27681391515142e-01 ) ( 2.62591137025923e-03 , -4.07263919254245e-04 , -1.85536278303028e-03 ) - 29 ( -3.13259948690306e-01 , 2.02495576423685e-01 , 9.27827433349212e-01 ) ( 2.62651989738061e-03 , -4.04991152847370e-04 , -1.85565486669842e-03 ) - 30 ( -3.13478176932022e-01 , 2.01398322580004e-01 , 9.27992536742261e-01 ) ( 2.62695635386404e-03 , -4.02796645160007e-04 , -1.85598507348452e-03 ) - 31 ( -3.13590843998619e-01 , 2.00357900935419e-01 , 9.28179666924991e-01 ) ( 2.62718168799724e-03 , -4.00715801870839e-04 , -1.85635933384998e-03 ) - 32 ( -3.13582621254546e-01 , 1.99390533269725e-01 , 9.28390733952867e-01 ) ( 2.62716524250909e-03 , -3.98781066539451e-04 , -1.85678146790573e-03 ) - 33 ( -3.13442157429236e-01 , 1.98510960989129e-01 , 9.28626626967630e-01 ) ( 2.62688431485847e-03 , -3.97021921978259e-04 , -1.85725325393526e-03 ) - 34 ( -3.13161736572708e-01 , 1.97732440207133e-01 , 9.28887296089519e-01 ) ( 2.62632347314542e-03 , -3.95464880414266e-04 , -1.85777459217904e-03 ) - 35 ( -3.12736895616453e-01 , 1.97066585116309e-01 , 9.29171886763036e-01 ) ( 2.62547379123291e-03 , -3.94133170232619e-04 , -1.85834377352607e-03 ) - 36 ( -3.12166051308255e-01 , 1.96522999367774e-01 , 9.29478922370005e-01 ) ( 2.62433210261651e-03 , -3.93045998735549e-04 , -1.85895784474001e-03 ) - 37 ( -3.11450199612716e-01 , 1.96108732516444e-01 , 9.29806505780634e-01 ) ( 2.62290039922543e-03 , -3.92217465032889e-04 , -1.85961301156127e-03 ) - 38 ( -3.10592727664091e-01 , 1.95827676730295e-01 , 9.30152502844880e-01 ) ( 2.62118545532818e-03 , -3.91655353460590e-04 , -1.86030500568976e-03 ) - 39 ( -3.09599357305329e-01 , 1.95680044131724e-01 , 9.30514673868571e-01 ) ( 2.61919871461066e-03 , -3.91360088263449e-04 , -1.86102934773714e-03 ) - 40 ( -3.08478219385086e-01 , 1.95662054939033e-01 , 9.30890728507939e-01 ) ( 2.61695643877017e-03 , -3.91324109878067e-04 , -1.86178145701588e-03 ) + 20 ( -3.10901117446188e-01 , 2.11904565128898e-01 , 9.26518726442291e-01 ) ( 7.94130223072518e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 21 ( -3.10816453337529e-01 , 2.11095512762292e-01 , 9.26731793361113e-01 ) ( 7.94069599606790e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 22 ( -3.10892396475955e-01 , 2.10199969837026e-01 , 9.26909861040409e-01 ) ( 7.94123977913618e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 23 ( -3.11100805214040e-01 , 2.09225106408128e-01 , 9.27060485536776e-01 ) ( 7.94273254820461e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 24 ( -3.11409297991705e-01 , 2.08181357553633e-01 , 9.27191874150890e-01 ) ( 7.94494348066520e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 25 ( -3.11783235003775e-01 , 2.07082512547608e-01 , 9.27312270687470e-01 ) ( 7.94762551358989e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 26 ( -3.12187603238500e-01 , 2.05945293478677e-01 , 9.27429477900170e-01 ) ( 7.95052836725782e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 27 ( -3.12588650041043e-01 , 2.04788513100117e-01 , 9.27550538120572e-01 ) ( 7.95341000358556e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 28 ( -3.12955168297890e-01 , 2.03632015427766e-01 , 9.27681553620888e-01 ) ( 7.95604583314044e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 29 ( -3.13259404950173e-01 , 2.02495635675013e-01 , 9.27827603999167e-01 ) ( 7.95823542608053e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 30 ( -3.13477605859996e-01 , 2.01398385322399e-01 , 9.27992716034892e-01 ) ( 7.95980674975593e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 31 ( -3.13590245146508e-01 , 2.00357967197589e-01 , 9.28179854946983e-01 ) ( 7.96061820008563e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 32 ( -3.13581994145287e-01 , 1.99390603070514e-01 , 9.28390930780262e-01 ) ( 7.96055875306068e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 33 ( -3.13441501552556e-01 , 1.98511034339754e-01 , 9.28626832667374e-01 ) ( 7.95954669919353e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 34 ( -3.13161051381254e-01 , 1.97732517113166e-01 , 9.28887510721228e-01 ) ( 7.95752740966183e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 35 ( -3.12736180522070e-01 , 1.97066665578977e-01 , 9.29172110381091e-01 ) ( 7.95447071123432e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 36 ( -3.12165305680866e-01 , 1.96523083384579e-01 , 9.29479155025108e-01 ) ( 7.95036822969748e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 37 ( -3.11449422780014e-01 , 1.96108820080825e-01 , 9.29806747521496e-01 ) ( 7.94523116380859e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 38 ( -3.10591918912976e-01 , 1.95827767830926e-01 , 9.30152753719685e-01 ) ( 7.93908878601734e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 39 ( -3.09598515885194e-01 , 1.95680138752022e-01 , 9.30514933926197e-01 ) ( 7.93198781048580e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) + 40 ( -3.08477344513251e-01 , 1.95662153057439e-01 , 9.30890997798872e-01 ) ( 7.92399262106393e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt index 08ab1004b..1b9427efe 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-fixed/namd-version.txt @@ -1 +1,3 @@ -Info: NAMD 2.11 for Linux-x86_64-multicore +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-10-05. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out index 5b55b80fb..3cd2a97fc 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.out @@ -1,13 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +49,7 @@ 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" @@ -59,28 +63,28 @@ 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: # 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: # 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,11 +119,13 @@ colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( -0.707107 , 0.707107 , 0 ) } +colvars: Initial step for restraint change: 0 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -131,14 +137,32 @@ 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: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped index 41cb47258..74d999a8a 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) + x ( -0.31090246767985 , 0.21190525235629 , 0.92651811618252 ) } restraint { configuration { step 20 name harmonic1 - firstStep 0 - centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) - accumulatedWork -1.32790918552119e-03 +firstStep 0 +centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) +accumulatedWork -6.04286529695808e-02 } } diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj index 4806fa83f..5f5447e79 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 2.66200013367620e-03 , -4.30091230223396e-04 , -1.83760097863971e-03 ) 5.32400026735240e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 - 1 ( -3.30748902386493e-01 , 2.14640582517095e-01 , 9.18985627693302e-01 ) ( 2.65426681755214e-03 , -2.59364533396170e-04 , -1.83797125538660e-03 ) 5.24527031778478e-03 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -4.11137793191958e-05 - 2 ( -3.30335278534755e-01 , 2.14351256281980e-01 , 9.19201905288334e-01 ) ( 2.61609431372619e-03 , -8.80022404594755e-06 , -1.83840381057667e-03 ) 5.11187773649830e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.11474667340389e-04 - 3 ( -3.29748301559333e-01 , 2.14175298816286e-01 , 9.19453641569650e-01 ) ( 2.49361536951405e-03 , 3.69150719454903e-04 , -1.83890728313930e-03 ) 4.86798493036677e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.40880322518690e-04 - 4 ( -3.28983003639496e-01 , 2.14104951472765e-01 , 9.19744123694835e-01 ) ( 2.15062069976169e-03 , 9.02948227784763e-04 , -1.83948824738967e-03 ) 4.41210095429392e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -4.77813021182742e-04 - 5 ( -3.28041627441930e-01 , 2.14127009680035e-01 , 9.20075167793771e-01 ) ( 1.42145011961404e-03 , 1.41950504566250e-03 , -1.84015033558754e-03 ) 3.71083413738751e-03 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -8.12629094252072e-04 - 6 ( -3.26934243989619e-01 , 2.14223123081484e-01 , 9.20446877144005e-01 ) ( 5.39673174025796e-04 , 1.56829094993247e-03 , -1.84089375428801e-03 ) 3.06983672648989e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -1.08583725325208e-03 - 7 ( -3.25678716875359e-01 , 2.14370596669932e-01 , 9.20857546343514e-01 ) ( -8.16417941512103e-05 , 1.43209521319758e-03 , -1.84171509268703e-03 ) 2.72473828242341e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -1.22624326781898e-03 - 8 ( -3.24300100426941e-01 , 2.14543773657555e-01 , 9.21303649210103e-01 ) ( -4.37177441924495e-04 , 1.25052160675694e-03 , -1.84260729842021e-03 ) 2.57506503044251e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -1.28775963537044e-03 - 9 ( -3.22829597532927e-01 , 2.14715908506054e-01 , 9.21779870463197e-01 ) ( -6.43292084741085e-04 , 1.09981786773007e-03 , -1.84355974092639e-03 ) 2.51106828341672e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -1.31512027126455e-03 - 10 ( -3.21303195136169e-01 , 2.14861254665660e-01 , 9.22279186601751e-01 ) ( -7.71607172100758e-04 , 9.84491053041776e-04 , -1.84455837320350e-03 ) 2.48349792685589e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 11 ( -3.19760075975256e-01 , 2.14956988805007e-01 , 9.22793035721544e-01 ) ( -7.74693410422582e-04 , 9.84299584763081e-04 , -1.84558607144309e-03 ) 2.48759174991084e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 12 ( -3.18240889009191e-01 , 2.14984610793561e-01 , 9.23311623280342e-01 ) ( -7.77731784354714e-04 , 9.84244340785974e-04 , -1.84662324656068e-03 ) 2.49181053275155e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 13 ( -3.16785934761420e-01 , 2.14930586280875e-01 , 9.23824395985673e-01 ) ( -7.80641692850256e-04 , 9.84352389811345e-04 , -1.84764879197135e-03 ) 2.49607856920830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 14 ( -3.15433317695425e-01 , 2.14786197242876e-01 , 9.24320675718985e-01 ) ( -7.83346926982245e-04 , 9.84641167887343e-04 , -1.84864135143797e-03 ) 2.50031274187874e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 15 ( -3.14217133435043e-01 , 2.14546757480910e-01 , 9.24790398906851e-01 ) ( -7.85779295503009e-04 , 9.85120047411276e-04 , -1.84958079781370e-03 ) 2.50442986834698e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 16 ( -3.13165766618895e-01 , 2.14210472267861e-01 , 9.25224878712619e-01 ) ( -7.87882029135306e-04 , 9.85792617837373e-04 , -1.85044975742524e-03 ) 2.50835474098607e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 17 ( -3.12300394959219e-01 , 2.13777265827330e-01 , 9.25617493311199e-01 ) ( -7.89612772454658e-04 , 9.86659030718436e-04 , -1.85123498662240e-03 ) 2.51202767450830e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 18 ( -3.11633818168871e-01 , 2.13247870196033e-01 , 9.25964205156089e-01 ) ( -7.90945926035354e-04 , 9.87717821981030e-04 , -1.85192841031218e-03 ) 2.51541039534613e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 19 ( -3.11169739281378e-01 , 2.12623380444018e-01 , 9.26263834684329e-01 ) ( -7.91874083810339e-04 , 9.88966801485059e-04 , -1.85252766936866e-03 ) 2.51848933241326e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 0 ( -3.31000066838099e-01 , 2.15045615111698e-01 , 9.18800489319855e-01 ) ( 8.08858571784670e-03 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 7.28214545131926e-03 ( 1.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) 0.00000000000000e+00 + 1 ( -3.30748901282821e-01 , 2.14640582611379e-01 , 9.18985628068499e-01 ) ( 7.91556346009634e-03 , 6.74933156844315e-04 , 0.00000000000000e+00 ) 7.12437272980631e-03 ( 9.96384506389575e-01 , 8.49583158190100e-02 , 0.00000000000000e+00 ) -7.92511683396072e-03 + 2 ( -3.30335274309661e-01 , 2.14351256826951e-01 , 9.19201906679630e-01 ) ( 7.54198086607204e-03 , 1.61954410896458e-03 , 0.00000000000000e+00 ) 6.86333398886249e-03 ( 9.77711878328341e-01 , 2.09951144259006e-01 , 0.00000000000000e+00 ) -1.55978590298878e-02 + 3 ( -3.29748292547839e-01 , 2.14175300340392e-01 , 9.19453644446465e-01 ) ( 6.72466310040318e-03 , 2.92398059373270e-03 , 0.00000000000000e+00 ) 6.40485416327734e-03 ( 9.17059383197694e-01 , 3.98750658543737e-01 , 0.00000000000000e+00 ) -2.28340233498076e-02 + 4 ( -3.28982988789206e-01 , 2.14104954582435e-01 , 9.19744128282738e-01 ) ( 5.02415671767963e-03 , 4.48057216346437e-03 , 0.00000000000000e+00 ) 5.60458335931272e-03 ( 7.46327346241351e-01 , 6.65579065365146e-01 , 0.00000000000000e+00 ) -2.93372355096835e-02 + 5 ( -3.28041606589159e-01 , 2.14127014682067e-01 , 9.20075174064462e-01 ) ( 2.29973244212613e-03 , 5.55204525161030e-03 , 0.00000000000000e+00 ) 4.49065525693204e-03 ( 3.82683432365090e-01 , 9.23879532511287e-01 , 0.00000000000000e+00 ) -3.49358204367317e-02 + 6 ( -3.26934217624704e-01 , 2.14223129394472e-01 , 9.20446885039306e-01 ) ( -3.13755411807546e-04 , 5.48610165814504e-03 , 0.00000000000000e+00 ) 3.57036392408472e-03 ( -5.70976569767208e-02 , 9.98368598047719e-01 , 0.00000000000000e+00 ) -4.00551555276943e-02 + 7 ( -3.25678685330811e-01 , 2.14370602957673e-01 , 9.20857556036089e-01 ) ( -1.92769172990675e-03 , 4.89375542981003e-03 , 0.00000000000000e+00 ) 3.10661161653516e-03 ( -3.66499613950964e-01 , 9.30418203268721e-01 , 0.00000000000000e+00 ) -4.51362604431086e-02 + 8 ( -3.24300063602745e-01 , 2.14543778409481e-01 , 9.21303661065688e-01 ) ( -2.80407252506292e-03 , 4.33767071287812e-03 , 0.00000000000000e+00 ) 2.91158490761996e-03 ( -5.42888821389189e-01 , 8.39804577036026e-01 , 0.00000000000000e+00 ) -5.02332493763967e-02 + 9 ( -3.22829555020146e-01 , 2.14715910294435e-01 , 9.21779884935621e-01 ) ( -3.30350461878850e-03 , 3.91937498024233e-03 , 0.00000000000000e+00 ) 2.82926231396191e-03 ( -6.44475639903469e-01 , 7.64624842371090e-01 , 0.00000000000000e+00 ) -5.53317735568784e-02 + 10 ( -3.21303146344621e-01 , 2.14861252199262e-01 , 9.22279204174317e-01 ) ( -3.61275538301498e-03 , 3.61275538301498e-03 , 0.00000000000000e+00 ) 2.79398931611509e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 11 ( -3.19760020211536e-01 , 2.14956980927590e-01 , 9.22793056879392e-01 ) ( -3.61449999241880e-03 , 3.61449999241880e-03 , 0.00000000000000e+00 ) 2.79921967120465e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 12 ( -3.18240825610009e-01 , 2.14984596391950e-01 , 9.23311648485630e-01 ) ( -3.61630000401958e-03 , 3.61630000401958e-03 , 0.00000000000000e+00 ) 2.80461232614324e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 13 ( -3.16785863094521e-01 , 2.14930564288528e-01 , 9.23824425677344e-01 ) ( -3.61812325535195e-03 , 3.61812325535195e-03 , 0.00000000000000e+00 ) 2.81007067874645e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 14 ( -3.15433237160699e-01 , 2.14786166642091e-01 , 9.24320710312994e-01 ) ( -3.61993425636311e-03 , 3.61993425636311e-03 , 0.00000000000000e+00 ) 2.81548844985626e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 15 ( -3.14217043465788e-01 , 2.14546717303910e-01 , 9.24790438796669e-01 ) ( -3.62169731639592e-03 , 3.62169731639592e-03 , 0.00000000000000e+00 ) 2.82075906487618e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 16 ( -3.13165666683135e-01 , 2.14210421596946e-01 , 9.25224924269859e-01 ) ( -3.62337999968208e-03 , 3.62337999968208e-03 , 0.00000000000000e+00 ) 2.82578596189438e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 17 ( -3.12300284560887e-01 , 2.13777203794208e-01 , 9.25617544886180e-01 ) ( -3.62495639995032e-03 , 3.62495639995032e-03 , 0.00000000000000e+00 ) 2.83049230626606e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 18 ( -3.11633696848677e-01 , 2.13247795980422e-01 , 9.25964263078181e-01 ) ( -3.62640972496061e-03 , 3.62640972496061e-03 , 0.00000000000000e+00 ) 2.83482860684602e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 19 ( -3.11169606617199e-01 , 2.12623293271569e-01 , 9.26263899262003e-01 ) ( -3.62773377317215e-03 , 3.62773377317215e-03 , 0.00000000000000e+00 ) 2.83877701143932e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 20 ( -3.10902467679847e-01 , 2.11905252356288e-01 , 9.26518116182517e-01 ) ( -3.62893305629181e-03 , 3.62893305629181e-03 , 0.00000000000000e+00 ) 2.84235157233888e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out index a610a83f9..73b13463c 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.out @@ -1,13 +1,16 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +49,7 @@ 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" @@ -59,28 +63,28 @@ 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: # 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: # 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: # 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: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -115,11 +119,13 @@ colvars: # writeTISamples = off [default] colvars: # writeTIPMF = off [default] colvars: # centers = { ( 1 , 0 , 0 ) } colvars: # targetCenters = { ( -0.707107 , 0.707107 , 0 ) } +colvars: Initial step for restraint change: 0 colvars: # targetNumSteps = 10 colvars: # targetNumStages = 0 [default] colvars: # outputAccumulatedWork = on colvars: # outputCenters = on colvars: # forceConstant = 0.001 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5). colvars: ---------------------------------------------------------------------- @@ -131,19 +137,37 @@ 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: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". -colvars: Restarting collective variable "one" from value: ( -0.310903 , 0.211905 , 0.926518 ) -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "one" from value: ( -0.310902 , 0.211905 , 0.926518 ) +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- 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 = 20, 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.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.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". diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped index e86a2eb4b..adeb0ffb2 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.state.stripped @@ -5,16 +5,16 @@ configuration { colvar { name one - x ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) + x ( -0.30848239239999 , 0.19566439197685 , 0.93088885442436 ) } restraint { configuration { step 40 name harmonic1 - firstStep 0 - centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) - accumulatedWork -1.32790918552119e-03 +firstStep 0 +centers ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) +accumulatedWork -6.04286529695808e-02 } } diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj index d4530bcd2..105070446 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one E_harmonic1 x0_one W_harmonic1 - 20 ( -3.10902612073186e-01 , 2.11905353216611e-01 , 9.26518044661955e-01 ) ( -7.92408338226723e-04 , 9.90402855939873e-04 , -1.85303608932391e-03 ) 2.52127576994097e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 21 ( -3.10818115103370e-01 , 2.11096376432417e-01 , 9.26731039288472e-01 ) ( -7.92577332166356e-04 , 9.92020809508261e-04 , -1.85346207857694e-03 ) 2.52380289534207e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 22 ( -3.10894230143356e-01 , 2.10200911472952e-01 , 9.26909032472718e-01 ) ( -7.92425102086384e-04 , 9.93811739427191e-04 , -1.85381806494544e-03 ) 2.52612036687898e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 23 ( -3.11102815077490e-01 , 2.09226128345936e-01 , 9.27059580430638e-01 ) ( -7.92007932218114e-04 , 9.95761305681222e-04 , -1.85411916086128e-03 ) 2.52828750263065e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 24 ( -3.11411487946955e-01 , 2.08182462090057e-01 , 9.27190890622198e-01 ) ( -7.91390586479184e-04 , 9.97848638192982e-04 , -1.85438178124440e-03 ) 2.53036637786130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 25 ( -3.11785608613730e-01 , 2.07083701948798e-01 , 9.27311207011189e-01 ) ( -7.90642345145636e-04 , 1.00004615847550e-03 , -1.85462241402238e-03 ) 2.53241596780659e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 26 ( -3.12190163793984e-01 , 2.05946569990115e-01 , 9.27428332508551e-01 ) ( -7.89833234785128e-04 , 1.00232042239286e-03 , -1.85485666501710e-03 ) 2.53448800783766e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 27 ( -3.12591400614140e-01 , 2.04789878956263e-01 , 9.27549309599856e-01 ) ( -7.89030761144815e-04 , 1.00463380446057e-03 , -1.85509861919971e-03 ) 2.53662475502718e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 28 ( -3.12958111790194e-01 , 2.03633472860108e-01 , 9.27680240705626e-01 ) ( -7.88297338792708e-04 , 1.00694661665288e-03 , -1.85536048141125e-03 ) 2.53885834955947e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 29 ( -3.13262544129311e-01 , 2.02497186917752e-01 , 9.27826205566553e-01 ) ( -7.87688474114472e-04 , 1.00921918853759e-03 , -1.85565241113311e-03 ) 2.54121118685469e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 30 ( -3.13480943392436e-01 , 2.01400032613720e-01 , 9.27991231097030e-01 ) ( -7.87251675588223e-04 , 1.01141349714565e-03 , -1.85598246219406e-03 ) 2.54369668144840e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 31 ( -3.13593783631662e-01 , 2.00359712776967e-01 , 9.28178282639445e-01 ) ( -7.87025995109772e-04 , 1.01349413681916e-03 , -1.85635656527889e-03 ) 2.54631998989969e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 32 ( -3.13585736154328e-01 , 1.99392449174349e-01 , 9.28389270345582e-01 ) ( -7.87042090064439e-04 , 1.01542866402440e-03 , -1.85677854069116e-03 ) 2.54907858621329e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 33 ( -3.13445449674932e-01 , 1.98512983197192e-01 , 9.28625083432615e-01 ) ( -7.87322663023230e-04 , 1.01718759597871e-03 , -1.85725016686523e-03 ) 2.55196288172193e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 34 ( -3.13165208280154e-01 , 1.97734570946912e-01 , 9.28885672069113e-01 ) ( -7.87883145812788e-04 , 1.01874442047927e-03 , -1.85777134413823e-03 ) 2.55495720640733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 35 ( -3.12740549003459e-01 , 1.97068826614834e-01 , 9.29170181713591e-01 ) ( -7.88732464366178e-04 , 1.02007590914343e-03 , -1.85834036342718e-03 ) 2.55804133355130e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 36 ( -3.12169888759603e-01 , 1.96525353868791e-01 , 9.29477135726621e-01 ) ( -7.89873784853888e-04 , 1.02116285463551e-03 , -1.85895427145324e-03 ) 2.56119257752050e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 37 ( -3.11454223752153e-01 , 1.96111202307429e-01 , 9.29804636919218e-01 ) ( -7.91305114868789e-04 , 1.02199115775824e-03 , -1.85960927383844e-03 ) 2.56438818134972e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 38 ( -3.10596941423876e-01 , 1.95830264173120e-01 , 9.30150551046453e-01 ) ( -7.93019679525344e-04 , 1.02255303402686e-03 , -1.86030110209291e-03 ) 2.56760755498004e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 39 ( -3.09603763986273e-01 , 1.95682751690521e-01 , 9.30512638289431e-01 ) ( -7.95006034400549e-04 , 1.02284805899205e-03 , -1.86102527657886e-03 ) 2.57083391329127e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 - 40 ( -3.08482822701290e-01 , 1.95664885198602e-01 , 9.30888608158067e-01 ) ( -7.97247916970515e-04 , 1.02288379197589e-03 , -1.86177721631613e-03 ) 2.57405494809733e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -1.32790918552119e-03 + 20 ( -3.10902467679847e-01 , 2.11905252356288e-01 , 9.26518116182517e-01 ) ( -3.62893305629181e-03 , 3.62893305629181e-03 , 0.00000000000000e+00 ) 2.84235157233888e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 21 ( -3.10817958631752e-01 , 2.11096261193422e-01 , 9.26731118017599e-01 ) ( -3.63002157106141e-03 , 3.63002157106141e-03 , 0.00000000000000e+00 ) 2.84559451102511e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 22 ( -3.10894061278729e-01 , 2.10200781201285e-01 , 9.26909118654028e-01 ) ( -3.63102048435833e-03 , 3.63102048435833e-03 , 0.00000000000000e+00 ) 2.84856927766063e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 23 ( -3.11102633537095e-01 , 2.09225982420665e-01 , 9.27059674285529e-01 ) ( -3.63195520689569e-03 , 3.63195520689569e-03 , 0.00000000000000e+00 ) 2.85135181992577e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 24 ( -3.11411293476549e-01 , 2.08182299919311e-01 , 9.27190992350319e-01 ) ( -3.63285241463941e-03 , 3.63285241463941e-03 , 0.00000000000000e+00 ) 2.85402171864755e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 25 ( -3.11785400983129e-01 , 2.07083522965549e-01 , 9.27311316791705e-01 ) ( -3.63373751356905e-03 , 3.63373751356905e-03 , 0.00000000000000e+00 ) 2.85665465646892e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 26 ( -3.12189942791681e-01 , 2.05946373647745e-01 , 9.27428450502286e-01 ) ( -3.63463284208611e-03 , 3.63463284208611e-03 , 0.00000000000000e+00 ) 2.85931708778741e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 27 ( -3.12591166041446e-01 , 2.04789664724126e-01 , 9.27549435952084e-01 ) ( -3.63555669333809e-03 , 3.63555669333809e-03 , 0.00000000000000e+00 ) 2.86206334977150e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 28 ( -3.12957863455182e-01 , 2.03633240219343e-01 , 9.27680375549326e-01 ) ( -3.63652302873947e-03 , 3.63652302873947e-03 , 0.00000000000000e+00 ) 2.86493482891272e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 29 ( -3.13262281841804e-01 , 2.02496935357561e-01 , 9.27826349025539e-01 ) ( -3.63754162872723e-03 , 3.63754162872723e-03 , 0.00000000000000e+00 ) 2.86796042686853e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 30 ( -3.13480666960014e-01 , 2.01399761628469e-01 , 9.27991383288821e-01 ) ( -3.63861841313708e-03 , 3.63861841313708e-03 , 0.00000000000000e+00 ) 2.87115753009954e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 31 ( -3.13593492856744e-01 , 2.00359421864171e-01 , 9.28178443677810e-01 ) ( -3.63975574358167e-03 , 3.63975574358167e-03 , 0.00000000000000e+00 ) 2.87453292651446e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 32 ( -3.13585430832281e-01 , 1.99392137833318e-01 , 9.28389440342786e-01 ) ( -3.64095266121656e-03 , 3.64095266121656e-03 , 0.00000000000000e+00 ) 2.87808353154779e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 33 ( -3.13445129592896e-01 , 1.98512650928049e-01 , 9.28625262501517e-01 ) ( -3.64220514295114e-03 , 3.64220514295114e-03 , 0.00000000000000e+00 ) 2.88179717045077e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 34 ( -3.13164873216125e-01 , 1.97734217249316e-01 , 9.28885860325330e-01 ) ( -3.64350651430441e-03 , 3.64350651430441e-03 , 0.00000000000000e+00 ) 2.88565382559024e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 35 ( -3.12740198724866e-01 , 1.97068450985727e-01 , 9.29170379277997e-01 ) ( -3.64484809952394e-03 , 3.64484809952394e-03 , 0.00000000000000e+00 ) 2.88962758493424e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 36 ( -3.12169523022357e-01 , 1.96524955799063e-01 , 9.29477342727713e-01 ) ( -3.64622012413799e-03 , 3.64622012413799e-03 , 0.00000000000000e+00 ) 2.89368933280031e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 37 ( -3.11453842298945e-01 , 1.96110781277138e-01 , 9.29804853495665e-01 ) ( -3.64761274877743e-03 , 3.64761274877743e-03 , 0.00000000000000e+00 ) 2.89780982034335e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 38 ( -3.10596543982360e-01 , 1.95829819645929e-01 , 9.30150777349381e-01 ) ( -3.64901704405092e-03 , 3.64901704405092e-03 , 0.00000000000000e+00 ) 2.90196255094194e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 39 ( -3.09603350267693e-01 , 1.95682283108234e-01 , 9.30512874484050e-01 ) ( -3.65042570939352e-03 , 3.65042570939352e-03 , 0.00000000000000e+00 ) 2.90612589840312e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 + 40 ( -3.08482392399995e-01 , 1.95664391976848e-01 , 9.30888854424365e-01 ) ( -3.65183337418098e-03 , 3.65183337418098e-03 , 0.00000000000000e+00 ) 2.91028398350180e-03 ( -7.07106781186548e-01 , 7.07106781186548e-01 , 0.00000000000000e+00 ) -6.04286529695808e-02 diff --git a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt index 617210efd..1b9427efe 100644 --- a/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt +++ b/namd/tests/library/000_distancedir_harmonic-ddir-moving/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-07-07". -colvars: Using NAMD interface, version "2020-05-04". +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-10-05. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out index f8931d8a7..619d1341d 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.out @@ -1,17 +1,25 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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.legacy.in": +colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -56,18 +64,13 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -95,6 +98,7 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,19 +109,36 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. -colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. -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: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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: - Custom functions (Lepton): +colvars: n/a +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, 2 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 "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. 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". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.state.stripped b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.state.stripped index d79f61955..69beeba1d 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x 1.57339203918876e+02 + x 155.48245218802 } restraint { diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.traj b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.traj index 9ef5589b1..d2271d40b 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.traj +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.colvars.traj @@ -1,4 +1,4 @@ # step c fa_c E_harmonic1 0 1.54436674571318e+02 2.65633254286824e-01 3.52805128915042e+00 - 10 1.55522973963020e+02 2.54770260369801e-01 3.24539427844480e+00 - 20 1.57339203918876e+02 2.36607960811239e-01 2.79916635596263e+00 + 10 1.54964141174777e+02 2.60358588252226e-01 3.38932972383461e+00 + 20 1.55482452188020e+02 2.55175478119796e-01 3.25572623168333e+00 diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out index fc34e52ef..c71a20a8c 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.out @@ -1,17 +1,25 @@ 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: 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: - Multiple replicas: enabled (replica number 1 of 1) +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.legacy.in": +colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 10 colvars: # colvarsRestartFrequency = 10 [default] colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "c" @@ -56,18 +64,13 @@ colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. colvars: This colvar uses a custom function. colvars: Warning: Variable r2 is absent from expression "atan2(r3, r1) * 180 / 3.1415926". -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r1. -colvars: Warning: Variable r1 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r3 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r2. -colvars: Warning: Variable r2 is absent from derivative of "atan2(r3, r1) * 180 / 3.1415926" wrt r3. colvars: Expecting colvar value of type scalar number. colvars: # period = 360 colvars: # wrapAround = 0 colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # upperBoundary = 0 [default] +colvars: # upperBoundary = 1 [default] colvars: # hardLowerBoundary = off [default] colvars: # hardUpperBoundary = off [default] colvars: # expandBoundaries = off [default] @@ -95,6 +98,7 @@ colvars: # centers = { -179 } colvars: # targetCenters = { -179 } [default] colvars: # outputCenters = off [default] colvars: # forceConstant = 0.01 +colvars: # decoupling = off [default] colvars: # targetForceConstant = -1 [default] colvars: The force constant for colvar "c" will be rescaled to 0.01 according to the specified width (1). colvars: ---------------------------------------------------------------------- @@ -105,24 +109,41 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 atoms in total). -colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. -colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. +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: - Harmonic colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +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: - Custom functions (Lepton): +colvars: n/a +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". -colvars: Restarting collective variable "c" from value: 157.339 -colvars: Restarting harmonic bias "harmonic1" from step number 20. +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "c" from value: 155.482 +colvars: Restarted harmonic bias "harmonic1" with step number 20. colvars: ---------------------------------------------------------------------- -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: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 2 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 = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "c":0/0. 1 atoms: total mass = 15.999, total charge = -0.51. colvars: Re-initialized atom group for variable "c":0/1. 1 atoms: total mass = 12.011, total charge = -0.27. 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: 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". diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.state.stripped index e17c334be..8c65cd8ad 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name c - x 1.62477922120804e+02 + x 156.78345999153 } restraint { diff --git a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.traj b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.traj index c31841c8f..715b86ff2 100644 --- a/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/028_periodic_custom_function/AutoDiff/test.restart.colvars.traj @@ -1,4 +1,4 @@ # step c fa_c E_harmonic1 - 20 1.57339203918876e+02 2.36607960811239e-01 2.79916635596263e+00 - 30 1.59522611534976e+02 2.14773884650238e-01 2.30639107638768e+00 - 40 1.62477922120804e+02 1.85220778791957e-01 1.71533684481494e+00 + 20 1.55482452188020e+02 2.55175478119796e-01 3.25572623168333e+00 + 30 1.55887189204085e+02 2.51128107959153e-01 3.15326633035719e+00 + 40 1.56783459991531e+02 2.42165400084687e-01 2.93220404990882e+00 diff --git a/namd/tests/library/028_periodic_custom_function/namd-version.txt b/namd/tests/library/028_periodic_custom_function/namd-version.txt index fb5cc08df..1b9427efe 100644 --- a/namd/tests/library/028_periodic_custom_function/namd-version.txt +++ b/namd/tests/library/028_periodic_custom_function/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 3.0alpha8 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2021-03-09". -colvars: Using NAMD interface, version "2021-03-02". +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-10-05. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/src/colvarcomp_distances.cpp b/src/colvarcomp_distances.cpp index 319190c38..6e97e276e 100644 --- a/src/colvarcomp_distances.cpp +++ b/src/colvarcomp_distances.cpp @@ -384,32 +384,30 @@ void colvar::distance_dir::apply_force(colvarvalue const &force) cvm::real const iprod = force.rvector_value * x.rvector_value; cvm::rvector const force_tang = force.rvector_value - iprod * x.rvector_value; - if (!group1->noforce) - group1->apply_force(-1.0 * force_tang); - - if (!group2->noforce) - group2->apply_force( force_tang); + if (!group1->noforce) { + group1->apply_force(-1.0 / dist_v.norm() * force_tang); + } + if (!group2->noforce) { + group2->apply_force( 1.0 / dist_v.norm() * force_tang); + } } -cvm::real colvar::distance_dir::dist2(colvarvalue const &x1, - colvarvalue const &x2) const +cvm::real colvar::distance_dir::dist2(colvarvalue const &x1, colvarvalue const &x2) const { - return (x1.rvector_value - x2.rvector_value).norm2(); + return x1.dist2(x2); } -colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1, - colvarvalue const &x2) const +colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1, colvarvalue const &x2) const { - return colvarvalue((x1.rvector_value - x2.rvector_value), colvarvalue::type_unit3vectorderiv); + return x1.dist2_grad(x2); } -colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1, - colvarvalue const &x2) const +colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const { - return colvarvalue((x2.rvector_value - x1.rvector_value), colvarvalue::type_unit3vectorderiv); + return x2.dist2_grad(x1); } diff --git a/src/colvars_version.h b/src/colvars_version.h index 5db618e80..f20519b29 100644 --- a/src/colvars_version.h +++ b/src/colvars_version.h @@ -1,3 +1,3 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2024-10-05" +#define COLVARS_VERSION "2024-10-11" #endif diff --git a/src/colvarvalue.cpp b/src/colvarvalue.cpp index 3b8077d2e..0a7223d9e 100644 --- a/src/colvarvalue.cpp +++ b/src/colvarvalue.cpp @@ -153,29 +153,6 @@ std::string const colvarvalue::type_keyword(Type t) } -size_t colvarvalue::num_df(Type t) -{ - switch (t) { - case colvarvalue::type_notset: - default: - return 0; break; - case colvarvalue::type_scalar: - return 1; break; - case colvarvalue::type_3vector: - return 3; break; - case colvarvalue::type_unit3vector: - case colvarvalue::type_unit3vectorderiv: - return 2; break; - case colvarvalue::type_quaternion: - case colvarvalue::type_quaternionderiv: - return 3; break; - case colvarvalue::type_vector: - // the size of a vector is unknown without its object - return 0; break; - } -} - - size_t colvarvalue::num_dimensions(Type t) { switch (t) { @@ -591,6 +568,97 @@ cvm::real operator * (colvarvalue const &x1, } +cvm::real colvarvalue::norm2() const +{ + switch (value_type) { + case colvarvalue::type_scalar: + return (this->real_value)*(this->real_value); + case colvarvalue::type_3vector: + case colvarvalue::type_unit3vector: + case colvarvalue::type_unit3vectorderiv: + return (this->rvector_value).norm2(); + case colvarvalue::type_quaternion: + case colvarvalue::type_quaternionderiv: + return (this->quaternion_value).norm2(); + case colvarvalue::type_vector: + if (elem_types.size() > 0) { + // if we have information about non-scalar types, use it + cvm::real result = 0.0; + size_t i; + for (i = 0; i < elem_types.size(); i++) { + result += (this->get_elem(i)).norm2(); + } + return result; + } else { + return vector1d_value.norm2(); + } + break; + case colvarvalue::type_notset: + default: + return 0.0; + } +} + + +cvm::real colvarvalue::sum() const +{ + switch (value_type) { + case colvarvalue::type_scalar: + return (this->real_value); + case colvarvalue::type_3vector: + case colvarvalue::type_unit3vector: + case colvarvalue::type_unit3vectorderiv: + return (this->rvector_value).x + (this->rvector_value).y + + (this->rvector_value).z; + case colvarvalue::type_quaternion: + case colvarvalue::type_quaternionderiv: + return (this->quaternion_value).q0 + (this->quaternion_value).q1 + + (this->quaternion_value).q2 + (this->quaternion_value).q3; + case colvarvalue::type_vector: + return (this->vector1d_value).sum(); + case colvarvalue::type_notset: + default: + return 0.0; + } +} + + +cvm::real colvarvalue::dist2(colvarvalue const &x2) const +{ + colvarvalue::check_types(*this, x2); + + switch (this->type()) { + case colvarvalue::type_scalar: + return (this->real_value - x2.real_value) * (this->real_value - x2.real_value); + case colvarvalue::type_3vector: + return (this->rvector_value - x2.rvector_value).norm2(); + case colvarvalue::type_unit3vector: { + cvm::rvector const &v1 = this->rvector_value; + cvm::rvector const &v2 = x2.rvector_value; + cvm::real const theta = cvm::acos(v1 * v2); + return theta * theta; + } + case colvarvalue::type_quaternion: + // angle between (*this) and x2 is the distance, the quaternion + // object has it implemented internally + return this->quaternion_value.dist2(x2.quaternion_value); + case colvarvalue::type_vector: + return (this->vector1d_value - x2.vector1d_value).norm2(); + case colvarvalue::type_unit3vectorderiv: + case colvarvalue::type_quaternionderiv: + cvm::error("Error: computing a squared-distance between two variables of type \"" + + type_desc(this->type()) + "\", for which it is not defined.\n", + COLVARS_BUG_ERROR); + case colvarvalue::type_notset: + default: + this->undef_op(); + return 0.0; + }; + + return 0.0; +} + + colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const { colvarvalue::check_types(*this, x2); @@ -600,25 +668,30 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const return 2.0 * (this->real_value - x2.real_value); case colvarvalue::type_3vector: return 2.0 * (this->rvector_value - x2.rvector_value); - case colvarvalue::type_unit3vector: - case colvarvalue::type_unit3vectorderiv: - { - cvm::rvector const &v1 = this->rvector_value; - cvm::rvector const &v2 = x2.rvector_value; - cvm::real const cos_t = v1 * v2; - return colvarvalue(2.0 * (cos_t * v1 - v2), colvarvalue::type_unit3vectorderiv); - } + case colvarvalue::type_unit3vector: { + cvm::rvector const &v1 = this->rvector_value; + cvm::rvector const &v2 = x2.rvector_value; + cvm::real const cos_t = v1 * v2; + return colvarvalue(2.0 * std::acos(cos_t) * -1.0 / cvm::sqrt(1.0 - cos_t * cos_t) * v2, + colvarvalue::type_unit3vectorderiv); + } case colvarvalue::type_quaternion: - case colvarvalue::type_quaternionderiv: return this->quaternion_value.dist2_grad(x2.quaternion_value); case colvarvalue::type_vector: return colvarvalue(2.0 * (this->vector1d_value - x2.vector1d_value), colvarvalue::type_vector); break; + case colvarvalue::type_unit3vectorderiv: + case colvarvalue::type_quaternionderiv: + cvm::error("Error: computing a squared-distance gradient between two variables of type \"" + + type_desc(this->type()) + "\", for which it is not defined.\n", + COLVARS_BUG_ERROR); case colvarvalue::type_notset: default: this->undef_op(); return colvarvalue(colvarvalue::type_notset); }; + + return colvarvalue(colvarvalue::type_notset); } diff --git a/src/colvarvalue.h b/src/colvarvalue.h index e8a6a849d..61f1bf718 100644 --- a/src/colvarvalue.h +++ b/src/colvarvalue.h @@ -109,9 +109,6 @@ class colvarvalue { /// User keywords for specifying value types in the configuration static std::string const type_keyword(Type t); - /// Number of degrees of freedom for each supported type - static size_t num_df(Type t); - /// Number of dimensions for each supported type (used to allocate vector1d_value) static size_t num_dimensions(Type t); @@ -671,87 +668,4 @@ inline cvm::vector1d const colvarvalue::as_vector() const } -inline cvm::real colvarvalue::norm2() const -{ - switch (value_type) { - case colvarvalue::type_scalar: - return (this->real_value)*(this->real_value); - case colvarvalue::type_3vector: - case colvarvalue::type_unit3vector: - case colvarvalue::type_unit3vectorderiv: - return (this->rvector_value).norm2(); - case colvarvalue::type_quaternion: - case colvarvalue::type_quaternionderiv: - return (this->quaternion_value).norm2(); - case colvarvalue::type_vector: - if (elem_types.size() > 0) { - // if we have information about non-scalar types, use it - cvm::real result = 0.0; - size_t i; - for (i = 0; i < elem_types.size(); i++) { - result += (this->get_elem(i)).norm2(); - } - return result; - } else { - return vector1d_value.norm2(); - } - break; - case colvarvalue::type_notset: - default: - return 0.0; - } -} - - -inline cvm::real colvarvalue::sum() const -{ - switch (value_type) { - case colvarvalue::type_scalar: - return (this->real_value); - case colvarvalue::type_3vector: - case colvarvalue::type_unit3vector: - case colvarvalue::type_unit3vectorderiv: - return (this->rvector_value).x + (this->rvector_value).y + - (this->rvector_value).z; - case colvarvalue::type_quaternion: - case colvarvalue::type_quaternionderiv: - return (this->quaternion_value).q0 + (this->quaternion_value).q1 + - (this->quaternion_value).q2 + (this->quaternion_value).q3; - case colvarvalue::type_vector: - return (this->vector1d_value).sum(); - case colvarvalue::type_notset: - default: - return 0.0; - } -} - - -inline cvm::real colvarvalue::dist2(colvarvalue const &x2) const -{ - colvarvalue::check_types(*this, x2); - - switch (this->type()) { - case colvarvalue::type_scalar: - return (this->real_value - x2.real_value)*(this->real_value - x2.real_value); - case colvarvalue::type_3vector: - return (this->rvector_value - x2.rvector_value).norm2(); - case colvarvalue::type_unit3vector: - case colvarvalue::type_unit3vectorderiv: - // angle between (*this) and x2 is the distance - return cvm::acos(this->rvector_value * x2.rvector_value) * cvm::acos(this->rvector_value * x2.rvector_value); - case colvarvalue::type_quaternion: - case colvarvalue::type_quaternionderiv: - // angle between (*this) and x2 is the distance, the quaternion - // object has it implemented internally - return this->quaternion_value.dist2(x2.quaternion_value); - case colvarvalue::type_vector: - return (this->vector1d_value - x2.vector1d_value).norm2(); - case colvarvalue::type_notset: - default: - this->undef_op(); - return 0.0; - }; -} - - #endif