From a5abe2a3301e9ecf2e58c335a8bfebcab8081571 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 21 Oct 2015 19:30:35 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14136 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_commands.html | 16 +-- doc/doc2/fix_ave_correlate.html | 10 +- doc/doc2/fix_ave_correlate_long.html | 159 +++++++++++++++++++++++++++ 3 files changed, 174 insertions(+), 11 deletions(-) create mode 100644 doc/doc2/fix_ave_correlate_long.html diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index a66760ca64..411376f9da 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -433,14 +433,14 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. package.

- - - - - - - - + + + + + + +
adapt/fepaddtorqueatcave/spatial/spheredrudedrude/transform/direct
drude/transform/reversecolvarsgleimdipilangevin/drude
langevin/efflb/fluidlb/momentumlb/pclb/rigid/pc/spherelb/viscous
mesomeso/stationarynph/effnpt/effnve/effnvt/eff
nvt/sllod/effphononpimdqbmsstqeq/reaxqmmm
qtbreax/c/bondsreax/c/speciessaed/vtksmdsmd/adjust/dt
smd/integrate/tlsphsmd/integrate/ulsphsmd/move/triangulated/surfacesmd/setvelsmd/tlsph/reference/configurationsmd/wall/surface
temp/rescale/effti/rsti/springttm/mod +
adapt/fepaddtorqueatcave/correlate/longave/spatial/spheredrude
drude/transform/directdrude/transform/reversecolvarsgleimdipi
langevin/drudelangevin/efflb/fluidlb/momentumlb/pclb/rigid/pc/sphere
lb/viscousmesomeso/stationarynph/effnpt/effnve/eff
nvt/effnvt/sllod/effphononpimdqbmsstqeq/reax
qmmmqtbreax/c/bondsreax/c/speciessaed/vtksmd
smd/adjust/dtsmd/integrate/tlsphsmd/integrate/ulsphsmd/move/triangulated/surfacesmd/setvelsmd/tlsph/reference/configuration
smd/wall/surfacetemp/rescale/effti/rsti/springttm/mod
diff --git a/doc/doc2/fix_ave_correlate.html b/doc/doc2/fix_ave_correlate.html index eda6a0785b..860459bdb4 100644 --- a/doc/doc2/fix_ave_correlate.html +++ b/doc/doc2/fix_ave_correlate.html @@ -23,7 +23,7 @@
  • Nrepeat = # of correlation time windows to accumulate -
  • Nfreq = calculate tine window averages every this many timesteps +
  • Nfreq = calculate time window averages every this many timesteps
  • one or more input values can be listed @@ -80,7 +80,10 @@ and average the correlation data over longer timescales. The resulting correlation values can be time integrated by variables or used by other output commands such as thermo_style -custom, and can also be written to a file. +custom, and can also be written to a file. See the +fix ave/correlate/long command for an +alternate method for computing correlation functions efficiently over +very long time windows.

    The group specified with this command is ignored. However, note that specified values may represent calculations performed by computes and @@ -337,7 +340,8 @@ minimization.

    Related commands:

    -

    compute, fix ave/time, fix +

    fix ave/correlate/long, +compute, fix ave/time, fix ave/atom, fix ave/spatial, fix ave/histo, variable

    diff --git a/doc/doc2/fix_ave_correlate_long.html b/doc/doc2/fix_ave_correlate_long.html new file mode 100644 index 0000000000..05f4526650 --- /dev/null +++ b/doc/doc2/fix_ave_correlate_long.html @@ -0,0 +1,159 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    fix ave/correlate/long command +

    +

    Syntax: +

    +
    fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... 
+
    + +

    Examples: +

    +
    fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+	  type upper title1 "My correlation data" nlen 15 ncount 3 
+
    +

    Description: +

    +

    This fix is similar in spirit and syntax to the fix +ave/correlate. However, this fix allows the +efficient calculation of time correlation functions on the fly over +extremely long time windows without too much CPU overhead, using a +multiple-tau method (Ramirez) that decreases the resolution +of the stored correlation function with time. +

    +

    The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. +

    +

    Each listed value can be the result of a compute or fix or the +evaluation of an equal-style variable. See the fix +ave/correlate doc page for details. +

    +

    The Nevery and Nfreq arguments specify on what timesteps the input +values will be used to calculate correlation data, and the frequency +with which the time correlation functions will be output to a file. +Note that there is no Nrepeat argument, unlike the fix +ave/correlate command. +

    +

    The optional keywords ncorr, nlen, and ncount are unique to this +command and determine the number of correlation points calculated and +the memory and CPU overhead used by this calculation. Nlen and +ncount determine the amount of averaging done at longer correlation +times. The default values nlen=16, ncount=2 ensure that the +systematic error of the multiple-tau correlator is always below the +level of the statistical error of a typical simulation (which depends +on the ensemble size and the simulation length). +

    +

    The maximum correlation time (in time steps) that can be reached is +given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation +times are discarded and not calculated. With the default values of +the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to +7864320 time steps. If longer correlation times are needed, the value +of ncorr should be increased. Using nlen=16 and ncount=2, with +ncorr=30, the maximum number of steps that can be correlated is +80530636808. If ncorr=40, correlation times in excess of 8e12 time +steps can be calculated. +

    +

    The total memory needed for each correlation pair is roughly +4*ncorr*nlen*8 bytes. With the default values of the parameters, this +corresponds to about 10 KB. +

    +

    For the meaning of the additional optional keywords, see the fix +ave/correlate doc page. +

    +

    Restart, fix_modify, output, run start/stop, minimize info: +

    +

    Since this fix in intended for the calculation of time correlation +functions over very long MD simulations, the information about this +fix is written automatically to binary restart files, so that the time +correlation calculation can continue in subsequent simulations. None +of the fix_modify options are relevant to this fix. +

    +

    No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy minimization. +

    +

    Restrictions: +

    +

    This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

    +

    Related commands: +

    +

    fix ave/correlate +

    +

    Default: none +

    +

    The option defaults for keywords that are also keywords for the fix +ave/correlate command are as follows: type = +auto, start = 0, no file output, title 1,2 = strings as described on +the fix ave/correlate doc page. +

    +

    The option defaults for keywords unique to this command are as +follows: ncorr=20, nlen=16, ncount=2. +

    +
    + + + +

    (Ramirez) J. Ramirez, S.K. Sukumaran, B. Vorselaars and +A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). +

    +