diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt index 9a5acb419a64df4ed4b0d1fbc0d3488f9f2b186b..6d1dce5578c0f24da2479a6baf44561134c83906 100644 --- a/CHANGES/Unreleased.txt +++ b/CHANGES/Unreleased.txt @@ -7,11 +7,14 @@ Include all fixes in branch 2.1 indicated in \ref CHANGES-2-1 . Changes from version 2.1 which are relevant for users: - Changes leading to incompatible behavior: - Labels of quantities calculates by \ref SPRINT have changed from <i>label</i>.coord_<i>num</i> to <i>label</i>.coord-<i>num</i> +- Added experimental OpenMP support, see \ref Openmp +- Added multiple time step integration for bias potentials, see \ref MTS - Link cells are now used in all multicolvars that involve \ref SwitchingFunctions. The link cell cutoff is set equal to 2.*\f$d_{\textrm{max}}\f$. Where \f$d_{\textrm{max}}\f$ is the (user-specified) point at which the switching function goes to zero. Users should always set this parameter when using a switching function in order to achieve optimal performance. - New actions + - \ref EFFECTIVE_ENERGY_DRIFT - \ref EXTENDED_LAGRANGIAN - \ref DFSCLUSTERING calculate the size of clusters - \ref DUMPMULTICOLVAR print out a multicolvar diff --git a/src/generic/EffectiveEnergyDrift.cpp b/src/generic/EffectiveEnergyDrift.cpp index 27ba388471ec2df614de4c6486e292757a6b1e59..f9714146683d5203854e88b327be53a0bc1e29c8 100644 --- a/src/generic/EffectiveEnergyDrift.cpp +++ b/src/generic/EffectiveEnergyDrift.cpp @@ -46,14 +46,27 @@ namespace generic{ //+PLUMEDOC GENERIC EFFECTIVE_ENERGY_DRIFT /* -Print the effective energy drift. +Print the effective energy drift described in Ref \cite Ferrarotti2015 -This is currently undocumented \par Examples -This is currently undocumented +This is to monitor the effective energy drift for a metadynamics +simulation on the Debye-Huckel energy. Since this variable is very expensive, +it could be conveniently computed every second step. +\verbatim +dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0 +METAD ARG=dh HEIGHT=0.5 SIGMA=0.1 PACE=500 STRIDE=2 +EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff +\endverbatim + +This is to monitor if a restraint is too stiff +\verbatim +d: DISTANCE ATOMS=10,20 +RESTRAINT ARG=d KAPPA=100000 AT=0.6 +EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff +\endverbatim */ //+ENDPLUMEDOC diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt index e4dbf2899edce676a7954002007a9498411ad2b1..c10a4b2a3afddb52fc23df42722c3d56257e94c9 100644 --- a/user-doc/Misc.txt +++ b/user-doc/Misc.txt @@ -137,8 +137,8 @@ Notice that: different order in summations. This should be harmless. - The optimum number of threads is not necessary "all of them", nor should be equal to the number of threads used to parallelize MD. -- Only a few CVs are parallelized with opemMP (currently, COORDINATION and - DHENERGY). +- Only a few CVs are parallelized with opemMP (currently, \ref COORDINATION and + \ref DHENERGY). - You might want to tune also the environmental variable PLUMED_CACHELINE_SIZE, by default 512, to set the size of cachelines on your machine. This is used by PLUMED to decrease the number of threads to be used in each loop so as to @@ -147,7 +147,22 @@ Notice that: \page MTS Multiple time stepping -This is currently undocumented. +By setting a STRIDE different from 1, you change how frequently +an action is calculated. In the case of actions such as \ref PRINT, this just +means how frequently you dump some quantity on the disk. +Notice that variables are only computed when necessary. Thus, +if a variable is only appearing as the argument of a \ref PRINT statement with +STRIDE=10, it will be computed every 10 steps. + +In a similar fashion, the STRIDE keyword can be used in a bias potential +so as to apply the bias potential every few steps. +In this case, forces from this bias potential are scaled up by +a factor equal to STRIDE. + +This technique can allow your simulation to run faster if you need +the apply a bias potential on some very expensive collective variable. + +The technique is discussed in details here \cite Ferrarotti2015 See also \subpage EFFECTIVE_ENERGY_DRIFT. diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib index c809b2f5e733f32999e7821d71a10da48dba719a..9dc51edeb2834d0a0ab6023fabd18cd651932116 100644 --- a/user-doc/bibliography.bib +++ b/user-doc/bibliography.bib @@ -2082,5 +2082,13 @@ DOI = {{10.1021/jp805039u}} } - +@article{Ferrarotti2015, + Author = {Marco Jacopo Ferrarotti, Sandro Bottaro, Andrea Perez-Villa, and Giovanni Bussi}, + Journal = {J. Chem. Theory Comput.}, + Number = {1}, + Pages = {139--146}, + Title = {Accurate Multiple Time Step in Biased Molecular Simulations}, + Volume = {11}, + Year = {2015} +}