View source: R/analysis_online.R

analysis_online | R Documentation |

`analysis_online`

is a function to analyse the online measurements
and output files of the tmLQCD software, see references. The function
operates on a subdirectory either passed via `rundir`

or automatically
constructed from the various function arguments. Depending on which
parts of the analysis are requested, this subdirectory is expected
to contain `onlinemeas.%06d`

files with online correlator measurements,
`output.data`

containing the plaquette and energy violation, amongst others
and `monomial-%02d.data`

with measurements of the extremal eigenvalues of the

analysis_online(L, Time, t1, t2, beta, kappa, mul, cg_col, evals_id, rundir, cg.ylim, type = "", csw = 0, musigma = 0, mudelta = 0, muh = 0, addon = "", skip = 0, rectangle = TRUE, plaquette = TRUE, dH = TRUE, acc = TRUE, trajtime = TRUE, omeas = TRUE, plotsize = 5, debug = FALSE, trajlabel = FALSE, title = FALSE, pl = FALSE, method = "uwerr", fit.routine = "optim", oldnorm = FALSE, S = 1.5, stat_skip = 0, omeas.samples = 1, omeas.stride = 1, omeas.avg = 1, omeas.stepsize = 1, evals.stepsize = 1, boot.R = 1500, boot.l = 2, outname_suffix = "", verbose = FALSE)

`L` |
integer. spatial lattice extent |

`Time` |
integer. temporal lattice extent |

`t1` |
integer. initial time of fit range |

`t2` |
integer. end time of fit range |

`beta` |
numeric. inverse squared gauge coupling |

`kappa` |
numeric. hopping parameter |

`mul` |
numeric. light sea twisted quark mass |

`cg_col` |
integer. column of CG iteration counts from |

`evals_id` |
Integer. Monomial ID of the monomial for which eigenvalues are measured.
Function will attempt to open |

`rundir` |
string. run directory. If not specified, run directory will be constructed automatically. See construct_onlinemeas_rundir for details. |

`cg.ylim` |
numeric. y-limits for CG iteration counts |

`type` |
string. Type specifier for the gauge action, this might be 'iwa' for Iwasaki, for example. |

`csw` |
numeric. clover coefficient |

`musigma` |
numeric. average 1+1 sea twisted quark mass |

`mudelta` |
numeric. splitting 1+1 sea twisted quark mass |

`muh` |
numeric. "heavy" twisted mass in the case of a |

`addon` |
string. addon to output filenames |

`skip` |
integer. number of initial measurements to skip in analysis |

`rectangle` |
boolean. If true, rectangle plaquettes are analysed |

`plaquette` |
boolean. If true, square plaquettes are analysed |

`dH` |
boolean. If true, delta H is analysed |

`acc` |
boolean. If true, the acceptance rate is analysed |

`trajtime` |
boolean. If true, the time per trajectory is analysed |

`omeas` |
boolean. If true, online measurements are analysed ( |

`plotsize` |
numeric. size of plots being generated |

`debug` |
boolean. provide debug information |

`trajlabel` |
boolean or string. If not |

`title` |
bolean or string. If not |

`pl` |
boolean. If set to |

`method` |
string. method to compute errors, can be "uwerr", "boot" or "all" |

`fit.routine` |
string. minimisation routine for chisq, can be "optim" |

`oldnorm` |
boolean. If |

`S` |
numeric. |

`stat_skip` |
integer. By passing this parameter, the various timeseries plots
will include |

`omeas.samples` |
integer. number of stochastic samples per online measurement |

`omeas.stride` |
integer. stride length in the reading of online measurements |

`omeas.avg` |
integer. Block average over this many subsequent measurements. |

`omeas.stepsize` |
integer. Number of trajectories between online measurements. Autocorrelation times of online measurement data will be scaled by this factor. |

`evals.stepsize` |
integer. Numer of trajectories between (strange-charm Dirac opertoar) eigenvalue measurements. Autocorrelation times of eigenvalues will be scaled by this factor. |

`boot.R` |
integer. number of bootstrap samples to use in bootstrap-based parts of analysis. |

`boot.l` |
integer. bootstrap block size |

`outname_suffix` |
string. suffix for output files |

`verbose` |
boolean. If |

a list is returned with all the accumulated results. Moreover, a
PDF file with statistics and analytics is created and the results
are written into .Rdata files. On the one hand, the result of the
call to the onlinemeas function is written to
`onlineout.%s.Rdata`

, where `%s`

is replaced with a label
built from meta information based on the arguments above.
On the other hand, summary data across many calls of this
function is silently accumulated in the file
`omeas.summary.Rdata`

which contains the named list 'resultsum' with
element names based on `rundir`

.

K. Jansen and C. Urbach, Comput.Phys.Commun. 180 (2009) 2717-2738

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