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giacomofiorin committed Oct 11, 2024
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14 changes: 14 additions & 0 deletions doc/colvars-refman-main.tex
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Expand Up @@ -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}
Expand Down Expand Up @@ -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}

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2 changes: 1 addition & 1 deletion doc/cv_version.tex
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@@ -1 +1 @@
\newcommand{\cvversion}{2024-10-05}
\newcommand{\cvversion}{2024-10-11}
60 changes: 47 additions & 13 deletions gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.out
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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:
Expand Down Expand Up @@ -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"
Expand All @@ -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.
Expand All @@ -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]
Expand All @@ -96,29 +108,51 @@ 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]
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: ----------------------------------------------------------------------
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".
2 changes: 1 addition & 1 deletion ...cs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.state.stripped
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Expand Up @@ -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 {
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42 changes: 21 additions & 21 deletions gromacs/tests/library/000_distancedir_harmonic-ddir-fixed/AutoDiff/test.colvars.traj
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@@ -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 )
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