Command Line Scripts

Quicklook

The quicklook directory has scripts that are used to quickly look at the data. The scripts are written in python and use the matplotlib library to plot the data. The scripts are:

dbVid

Creates visualization of ground dB NOTE: Assumes ground dB has been calculated using calcdb.x on simulation data.

usage: dbVid [-h] [-d directory] [-o directory] [-id runid] [-nS Step-Start]
             [-nE Step-End] [-k0 layer] [-Nblk Nblk] [-nID nID]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-o <directory>: Subdirectory to write to (default: vid2D)

-id <runid>: RunID of data (default: msphere)

-nS <step-start>: Starting step (default: 0)

-nE <step-end>: Ending step (default: -1)

-k0 <layer>: Vertical layer to plot (default: 0)

-Nblk <nblk>: Number of job blocks (default: 1)

-nID <nid>: Block ID of this job [1-Nblk] (default: 1)

dstpic

Creates simple plot comparing SYM-H from OMNI dataset to Gamera-RCM. Need to run or point to directory that has the bcwind and msphere.gam files of interest. Note this calculation only includes the magnetospheric currents and does not include the ionospheric currents or the FACS. It should be used with CAUTION and never in a scientific publication.

usage: dstpic [-h] [-d directory] [-id runid] [-tpad time padding]
              [-swfile filename] [--dps]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: RunID of data (default: msphere)

-tpad <time padding>: Time beyond MHD data (in hours) to plot (default: 8)

-swfile <filename>: Solar wind file name (default: bcwind.h5)

--dps: Also plot the DPS Dst (default: False)

gamerrpic

Creates simple multi-panel figure for Gamera magnetosphere run Left Panel - Residual vertical magnetic field Right Panel - Pressure (or density) and hemispherical insets

usage: gamerrpic [-h] [-d1 directory1] [-id1 runid1] [-d2 directory2]
                 [-id2 runid2] [-n nStp] [-f fieldnames]
                 [-size {small,std,big,bigger,fullD,dm}]

-h, --help: show this help message and exit

-d1 <directory1>: Directory to read first dataset from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id1 <runid1>: RunID of first dataset (default: msphere)

-d2 <directory2>: Directory to read second dataset from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id2 <runid2>: RunID of second dataset (default: msphere)

-n <nstp>: Step number to plot (default: 1)

-f <fieldnames>: Comma-separated fields to plot (default: Bx, By, Bz)

-size {small,std,big,bigger,fullD,dm}: Domain bounds options (default: std)

gamerrVid

Creates simple multi-panel figure for Gamera magnetosphere run Left Panel - Residual vertical magnetic field Right Panel - Pressure (or density) and hemispherical insets

usage: gamerrVid [-h] [-d1 directory] [-id1 runid] [-d2 directory]
                 [-id2 runid] [-o directory] [-ts tStart] [-te tEnd] [-dt dt]
                 [-Nth Nth] [-f fieldnames] [-linear] [-v] [-skipMovie]

-h, --help: show this help message and exit

-d1 <directory>: Directory to read first dataset from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id1 <runid>: RunID of first dataset (default: msphere)

-d2 <directory>: Directory to read second dataset from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id2 <runid>: RunID of second dataset (default: msphere)

-o <directory>: Subdirectory to write to (default: vid2D)

-ts <tstart>: Starting time [min] (default: 0)

-te <tend>: Ending time [min] (default: 200)

-dt <dt>: Cadence [sec] (default: 0.0)

-Nth <nth>: Number of threads to use (default: 1)

-f <fieldnames>: Comma-separated fields to plot (default: Bx, By, Bz)

-linear: Plot linear line plot instead of logarithmic (default: False)

-v: Do verbose output (default: False)

-skipMovie: Skip automatic movie generation afterwards (default: False)

gamsphVid

Creates simple multi-panel figure for Gamera magnetosphere run Left Panel - Residual vertical magnetic field Right Panel - Pressure (or density) and hemispherical insets

usage: gamsphVid [-h] [-d directory] [-id runid] [-o directory] [-ts tStart]
                 [-te tEnd] [-dt dt] [-Nblk Nblk] [-nID nID] [-bz] [-jy]
                 [-bigrcm] [-noion] [-norcm]
                 [-size {small,std,big,bigger,fullD,dm}]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: RunID of data (default: msphere)

-o <directory>: Subdirectory to write to (default: vid2D)

-ts <tstart>: Starting time [min] (default: 0)

-te <tend>: Ending time [min] (default: 200)

-dt <dt>: Cadence [sec] (default: 60.0)

-Nblk <nblk>: Number of job blocks (default: 1)

-nID <nid>: Block ID of this job [1-Nblk] (default: 1)

-bz: Show Bz instead of dBz (default: False)

-jy: Show Jy instead of pressure (default: False)

-bigrcm: Show entire RCM domain (default: False)

-noion: Don’t show ReMIX data (default: False)

-norcm: Don’t show RCM data (default: False)

-size {small,std,big,bigger,fullD,dm}: Domain bounds options (default: std)

heliomovie

Make a movie from a gamhelio run

usage: heliomovie [-h] [--clobber] [--debug] [--directory directory]
                  [--first_step n0] [--hgsplot] [--jslice jSlice]
                  [--last_step n1] [--movie_format movie_format]
                  [--pictype pictype] [--runid runid]
                  [--spacecraft spacecraft] [--verbose]

-h, --help: show this help message and exit

--clobber: Overwrite existing frame and movie files (default: False).

--debug: Print debugging output (default: False).

--directory <directory>, -d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

--first_step <n0>, -n0 <n0>: First time step to plot (default: 1)

--hgsplot: Plot in the Heliographic Stonyhurst frame corresponding to the date of the plot (default: False).

--jslice <jslice>, -jslice <jslice>: Index of j-slice for pic7 (default: Nj/2-1)

--last_step <n1>, -n1 <n1>: Last time step to plot (default: -1)

--movie_format <movie_format>: Output movie format (default: mp4)

--pictype <pictype>, -p <pictype>: Code for plot type (default: pic1)

--runid <runid>, -id <runid>: Run ID of data (default: wsa)

--spacecraft <spacecraft>: Names of spacecraft to plot positions, separated by commas (default: None)

--verbose, -v: Print verbose output (default: False).

heliopic

Make a quicklook plot for a gamhelio run.

usage: heliopic [-h] [--debug] [--directory directory] [--hgsplot] [-id runid]
                [-jslice jSlice] [-lon lon] [--nlist list of steps]
                [--nslice step slice] [--nworkers nworkers] [--parallel]
                [-pic pictype] [--spacecraft spacecraft] [--verbose] [--inner]

-h, --help: show this help message and exit

--debug: Print debugging output (default: False).

--directory <directory>, -d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

--hgsplot: Plot in the Heliographic Stonyhurst frame corresponding to the date of the plot (default: False).

-id <runid>: Run ID of data (default: wsa)

-jslice <jslice>: Index of j-slice for pic7 (default: Nj/2-1)

-lon <lon>: Longitude of meridian slice (pic2) (default: 0.0)

--nlist <list of steps>: List of time slice(s) n1,n2,… to plot (default: 1)

--nslice <step slice>: Slice for range of time slice(s) n1:n2 to plot (default: None)

--nworkers <nworkers>, -nw <nworkers>: Number of parallel workers (default: 4)

--parallel, -p: Read from HDF5 in parallel (default: False).

-pic <pictype>: Code for plot type (pic1-pic7) (default: pic1)

--spacecraft <spacecraft>: Names of spacecraft to plot positions, separated by commas (valid spacecraft are ACE,STEREO_A,STEREO_B,Parker_Solar_Probe,Solar_Orbiter) (default: None)

--verbose, -v: Print verbose output (default: False).

--inner: Plot inner i-slice for pic3 (default: False).

mixpic

Creates simple multi-panel REMIX figure for a GAMERA magnetosphere run. Top Row - FAC (with potential contours overplotted), Pedersen and Hall Conductances Bottom Row - Joule heating rate, particle energy and energy flux

usage: mixpic [-h] [--debug] [-id runid] [-n step] [-nflux] [-print]
              [--spacecraft spacecraft] [-v] [-GTYPE] [-PP] [-vid]
              [-overwrite] [--ncpus ncpus] [-nohash] [--coord coord]

-h, --help: show this help message and exit

--debug: Print debugging output (default: False).

-id <runid>: Run ID of data (default: msphere)

-n <step>: Time slice to plot (default: -1)

-nflux: Show number flux instead of energy flux (default: False)

-print: Print list of all steps and time labels, then exit (default: False)

--spacecraft <spacecraft>: Names of spacecraft to plot magnetic footprints, separated by commas (default: None)

-v, --verbose: Print verbose output (default: False).

-GTYPE: Show RCM grid type in the eflx plot (default: False)

-PP: Show plasmapause (10/cc) in the eflx/nflx plot (default: False)

-vid: Make a video and store in mixVid directory (default: False)

-overwrite: Overwrite existing vid files (default: False)

--ncpus <ncpus>: Number of threads to use with –vid (default: 1)

-nohash: Don’t display branch/hash info (default: False)

--coord <coord>: Coordinate system to use (default: SM)

msphpic

Creates simple multi-panel figure for Gamera magnetosphere run Top Panel - Residual vertical magnetic field Bottom Panel - Pressure (or density) and hemispherical insets NOTE: There is an optional -size argument for domain bounds options (default: std), which is passed to kaiViz functions.

usage: msphpic [-h] [--debug] [-d directory] [-id runid] [-n step] [-bz]
               [-den] [-jy] [-ephi] [-noion] [-nompi] [-noIM] [-bigIM] [-src]
               [-v] [--spacecraft spacecraft] [-vid] [-overwrite]
               [--ncpus ncpus] [-nohash]
               [-size {small,std,big,bigger,fullD,dm}]

-h, --help: show this help message and exit

--debug: Print debugging output (default: False).

-d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: Run ID of data (default: msphere)

-n <step>: Time slice to plot (default: -1)

-bz: Show Bz instead of dBz (default: False).

-den: Show density instead of pressure (default: False).

-jy: Show Jy instead of pressure (default: False).

-ephi: Show Ephi instead of pressure (default: False).

-noion: Don’t show ReMIX data (default: False).

-nompi: Don’t show MPI boundaries (default: False).

-noIM: Don’t show Inner Mag data (default: False).

-bigIM: Show entire Inner Mag domain (default: False).

-src: Show source term (default: False).

-v, --verbose: Print verbose output (default: False).

--spacecraft <spacecraft>: Names of spacecraft to plot positions, separated by commas (default: None)

-vid: Make a video and store in mixVid directory (default: False)

-overwrite: Overwrite existing vid files (default: False)

--ncpus <ncpus>: Number of threads to use with –vid (default: 1)

-nohash: Don’t display branch/hash info (default: False)

-size {small,std,big,bigger,fullD,dm}: Domain bounds options (default: std)

raijupic

Creates simple multi-panel RAIJU figure MAGE run.

usage: raijupic [-h] [-d directory] [-id runid] [-n step] [-ns startstep]
                [-dn stride] [-uts %Y-%m-%dT%H:%M:%S.%f]
                [-ut %Y-%m-%dT%H:%M:%S.%f] [-domain {ACTIVE,BUFFER}] [-diff]
                [-v] [-vid] [-vidOut dir] [-overwrite] [-nohash]
                [--ncpus NCPUS]

-h, --help: show this help message and exit

-d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: Run ID of data (default: msphere)

-n <step>, -ne <step>: Time slice to plot (last slice if video; default: -1)

-ns <startstep>: First slice of video; default: 1)

-dn <stride>: Step stride in case of vid (default: 10)

-uts <%y-%m-%dt%h:%m:%s.%f>: First UT of video (default: -1)

-ut <%y-%m-%dt%h:%m:%s.%f>, -ute <%y-%m-%dt%h:%m:%s.%f>: UT to plot (overrides -n if provided; last UT if video; default: -1)

-domain {ACTIVE,BUFFER}: Domain to include (always includes active) (default: ACTIVE)

-diff: Do difference of some quantities from dipole (default: False)

-v, --verbose: Print verbose output (default: False).

-vid: Make a video and store in mixVid directory (default: False)

-vidOut <dir>: Output directory if doing video (default: qkRaijuVid)

-overwrite: Overwrite existing vid files (default: False)

-nohash: Don’t display branch/hash info (default: False)

--ncpus <ncpus>: Number of threads for parallel vid (default: 1)

rcmDataProbe

Plots RCM data at a given equatorial x,y,z point.

usage: rcmDataProbe [-h] [-id runid] [-n numSamples] [-t times] [-l loc] [-e]
                    [-v {specFlux,precipSpecFlux,den,press}]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-n <numsamples>: Number of evenly-spaced time samples (default: 6)

-t <times>: Comma-separated times (in hours) to plot (example: 1,2,4,6). Ignores numSamples

-l <loc>: Comma-separated x,y,z values for equatorial location (default: -5,0,0)

-e: Flag to plot electrons instead of ions (default: False)

-v {specFlux,precipSpecFlux,den,press}: Variable to plot (default: specFlux)

rcmpic

Creates simple multi-panel figure for RCM magnetosphere run Top Panel - XXX Bottom Panel - XXX

usage: rcmpic [-h] [-beta] [-big] [-bmin] [--debug] [-d directory] [-elec]
              [-fac] [-id runid] [-kt] [-n step] [--spacecraft spacecraft]
              [-tbnc] [-v] [-vol] [-wgt] [-vid] [-overwrite] [--ncpus ncpus]
              [-nohash]

-h, --help: show this help message and exit

-beta: Show beta instead of FTE (default: False)

-big: Show entire RCM grid (default: False).

-bmin: Show B-min (default: False)

--debug: Print debugging output (default: False).

-d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-elec: Show electron pressure (default: False)

-fac: Show FAC (default: False)

-id <runid>: Run ID of data (default: msphere)

-kt: Show temperature instead of FTE (default: False)

-n <step>: Time slice to plot (default: -1)

--spacecraft <spacecraft>: Names of spacecraft to plot trajectories, separated by commas (default: None)

-tbnc: Show Tb instead of FTE (default: False)

-v, --verbose: Print verbose output (default: False).

-vol: Show FTV instead of FTE (default: False)

-wgt: Show wRCM instead of FTE (default: False)

-vid: Make a video and store in mixVid directory (default: False)

-overwrite: Overwrite existing vid files (default: False)

--ncpus <ncpus>: Number of threads to use with –vid (default: 1)

-nohash: Don’t display branch/hash info (default: False)

remixTimeSeries

Creates a summary plot of global ionospheric paramters including CPCP, HP, FAC. Creates a PNG image file, python pickle file as well as a HDF5 file with the data.

usage: remixTimeSeries [-h] [-id runid] [-path path]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-path <path>: Path to directory containing REMIX files (default: .)

swpic

Creates simple multi-panel figure for the solar wind conditions with the bcwind file and saves it as swBCplot.imgtype

usage: swpic [-h] [-d directory] [-id swid] [-type type]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <swid>: Solar wind file used (default: bcwind.h5)

-type <type>: Image type (default: png)

vizTrj

Plots trajectory of specified CHIMP particle in H5p file ID: Particle ID Color specified by energy [keV]

usage: vizTrj [-h] [-id id] input.h5part

input.h5part: Input H5Part file

-h, --help: show this help message and exit

-id <id>: Display particle trajectory w/ given ID (default: 0)

Preprocessing

The preprocessing directory has scripts that are used to setup MAGE simulations including grid generation and solar wind input file. The scripts are:

cda2wind

This script does several things: 1. Fetch OMNI data from CDAWeb between the specified times (must be at least 2 hours in length) 2. Generate standard plots of solar wind data 3. Write output in a model file format.

“LFM” format will:

Generate coefficients for Bx Fit

Save a bcwind.h5 file

“TIEGCM” format will:

Compute 15-minute boxcar average lagged by 5 minutes

Sub-sample at 5-minutes

Write NetCDF IMF data file

usage: cda2wind [-h] [-t0 TStart] [-t1 TStop] [-obs OMNI] [-offset tOffset]
                [-o wind.h5] [-m LFM] [-TsG GAMERA_TStart] [-TsL LFM_TStart]
                [-bx] [-bs] [-interp] [-filter] [-sig sigma] [-eps]
                [-fn filename] [-f107 F107] [-kp KP] [-safe]

-h, --help: show this help message and exit

-t0 <tstart>: Start time in ‘YYYY-MM-DDThh:mm:ss’ (default: 2010-01-01T00:00:00)

-t1 <tstop>: End time in ‘YYYY-MM-DDThh:mm:ss’ (default: 2010-01-01T02:00:00)

-obs <omni>: Select spacecraft to obtain observations from (default: OMNI)

-offset <toffset>: Minutes to offset spacecraft observation and simulation t0 (default: 0.0)

-o <wind.h5>: Output Gamera wind file (default: bcwind.h5)

-m <lfm>: Format to write. Options are LFM or TIEGCM (default: LFM)

-TsG <gamera_tstart>: Gamera start time [min] (default: 0.0)

-TsL <lfm_tstart>: LFM start time [min] (default: 0.0)

-bx: Include Bx through ByC and BzC fit coefficients (default: False)

-bs: Include Bowshock location (default: True)

-interp: Include shaded region on plots where data is interpolated (default: False)

-filter: Include additional filtering of data to remove outlier points (default: False)

-sig <sigma>: N used in N*sigma used for filtering threshold above which will be thrown out (default: 3.0)

-eps: Output eps figure. (default: False)

-fn <filename>: Name of Wind file. Only used if obs is WINDF. (default: None)

-f107 <f107>: Set f10.7 value to use in bcwind file. Only used if no data available. (default: None)

-kp <kp>: Set Kp value to use in bcwind file. Only used if no data available. (default: None)

-safe: Run in SAFE mode. Does not create the h5 file if certain conditions are not met (default: False)

genLFM

Generates LFM-style HDF5 grid for Gamera Grid types (gid) D: Double ( 48, 48, 64) Q: Quad ( 96, 96,128) O: Oct (192,192,256) H: Hex (384,384,512)

usage: genLFM [-h] [-gid {D,Q,O,H}] [-viz] [-chimp] [-Rin Rin] [-Rout Rout]
              [-vizG]

-h, --help: show this help message and exit

-gid {D,Q,O,H}: Grid Resolution Specifier (default: D)

-viz: Show 2D figure of grid (default: False)

-chimp: Store grid in CHIMP format (default: False)

-Rin <rin>: Inner radius (default: 2.0)

-Rout <rout>: Sunward outer radius (default: 0.0)

-vizG: Show 2D figure w/ ghosts (default: False)

genRCM

Generates RCM configuration data

usage: genRCM [-h] [-o fOut] [-ne NE] [-np NP] [-mine MINE] [-minp MINP]
              [-maxe MAXE] [-maxp MAXP] [-L L] [-p1 P1] [-p2 P2]
              [-plotType {none,spec,vs}] [--nop] [--noWaveModel] [--addWM]
              [-maxKp MAXKP] [-i fIn]

-h, --help: show this help message and exit

-o <fout>: Output file name (default: rcmconfig.h5)

-ne <ne>: Number of electron channels (default: 39)

-np <np>: Number of proton channels (default: 120)

-mine <mine>: Min. energy [eV] for electrons at L_kt (default: 1)

-minp <minp>: Min. energy [eV] for protons at L_kt (default: 1)

-maxe <maxe>: Max. energy [keV] for electrons at L_kt (default: 25)

-maxp <maxp>: Max. energy [keV] for protons at L_kt (default: 100)

-L <l>: L shell [R_e] at which kt should be resolved (default: 10 [R_e])

-p1 <p1>: Wolf low-energy p* (default: 3)

-p2 <p2>: Wolf high-energy p* (default: 1)

-plotType {none,spec,vs}: Plot mode (default: none)

--nop: Do not add zero loss first channel (default: False)

--noWaveModel: Don’t use wave models in the electron/ion loss (default: False)

--addWM: Add wave models to an existing rcmconfig file, input file needed to be presented (default: False)

-maxKp <maxkp>: Max. Kp index allowed in the electron wave model, integer only (default: 6)

-i <fin>: Input file name when addWM is true (default: rcmconfig.h5)

genRAIJU

Generates RAIJU configuration data

usage: genRAIJU [-h] [-o fOut] [-ne NE] [-np NP] [-mine MINE] [-minp MINP]
                [-maxe MAXE] [-maxp MAXP] [-L L] [-p1 P1] [-p2 P2]
                [-plotType {none,spec,vs}] [-npSpc NPSPC] [--nop]
                [--noWaveModel] [--append]

-h, --help: show this help message and exit

-o <fout>: Output file name (default: raijuconfig.h5)

-ne <ne>: Number of electron channels (default: 39)

-np <np>: Number of proton channels (default: 120)

-mine <mine>: Min. energy [eV] for electrons at L_kt (default: 1)

-minp <minp>: Min. energy [eV] for protons at L_kt (default: 1)

-maxe <maxe>: Max. energy [keV] for electrons at L_kt (default: 25)

-maxp <maxp>: Max. energy [keV] for protons at L_kt (default: 100)

-L <l>: L shell [R_e] at which kt should be resolved (default: 10 [R_e])

-p1 <p1>: Wolf low-energy p* (default: 3)

-p2 <p2>: Wolf high-energy p* (default: 1)

-plotType {none,spec,vs}: Plot mode (default: none)

-npSpc <npspc>: Number of proton species to include (default: 1)

--nop: Do not add zero energy first channel (default: False)

--noWaveModel: Don’t use wave models in the electron/ion loss (default: False)

--append: Append existing file rather than make a new one (default: False)

wsa2gamera

Convert WSA FITS output to gamhelio format.

usage: wsa2gamera [-h] [--debug] [--verbose] ConfigFileName

configfilename: Name of the configuration file to use (default: startup.config).

-h, --help: show this help message and exit

--debug, -d: Print debugging output (default: False).

--verbose, -v: Print verbose output (default: False).

XMLGenerator

Convert Kaiju .ini files to XML configuration or XML configuration template files.

usage: XMLGenerator [-h] [-t TEMPLATE] [-d] [-v] ini_file xml_file

ini_file: Path to .ini file to convert

xml_file: Path to .xml file output

-h, --help: show this help message and exit

-t <template>: Path to .xml file as source template

-d, --debug: Activate debug mode

-v, --verbose: Activate verbose execution mode

Postprocessing

The postprocessing directory has scripts that are used to process MAGE simulations including data analysis and visualization. The scripts are:

embiggen

Upscales and retiles a Gamera MPI resart

(iRi,iRj,iRk) : Input MPI decomposition (oRi,oRj,oRk) : Output MPI decomposition inid/nres : Run ID string and restart number, i.e. input file = inid.MPISTUFF.Res.#nres.h5 outid : Output Run ID grid : Filename of input grid corners file (with ghosts) generated by genLFM/genGrid

usage: embiggen [-h] [-i inid] [-n nres] [-iRi iRi] [-iRj iRj] [-iRk iRk]
                [-o outid] [-oRi oRi] [-oRj oRj] [-oRk oRk] [-grid grid]
                [--keep] [--norescale] [--down]

-h, --help: show this help message and exit

-i <inid>: Input Run ID string (default: msphere)

-n <nres>: Restart number (default: 0)

-iRi <iri>: Input i-Ranks (default: 4)

-iRj <irj>: Input j-Ranks (default: 4)

-iRk <irk>: Input k-Ranks (default: 1)

-o <outid>: Output run ID (default: msphere)

-oRi <ori>: Input i-Ranks (default: 8)

-oRj <orj>: Input j-Ranks (default: 8)

-oRk <ork>: Input k-Ranks (default: 1)

-grid <grid>: inGrid file to read from (default: lfmQ.h5)

--keep: Keep intermediate files (default: False)

--norescale: Do not rescale (up or down) (default: False)

--down: Downscale instead of upscale (default: False)

embiggenMIX

Up/down-scales a ReMIX restart

inid/nres : Run ID string and restart number, i.e. input file = inid.MPISTUFF.Res.#nres.h5 outid : Output Run ID

usage: embiggenMIX [-h] [-i inid] [-n nres] [-o outid] [--down]

-h, --help: show this help message and exit

-i <inid>: Input Run ID string (default: msphere)

-n <nres>: Restart number (default: 0)

-o <outid>: Output run ID (default: msphereX)

--down: Downscale instead of upscale (default: False)

embiggenRCM

Up/down-scales a RCM restart (kinda)

inid/nres : Run ID string and restart number, i.e. input file = inid.MPISTUFF.Res.#nres.h5 outid : Output Run ID

usage: embiggenRCM [-h] [-i inid] [-n nres] [-o outid] [--down]

-h, --help: show this help message and exit

-i <inid>: Input Run ID string (default: msphere)

-n <nres>: Restart number (default: 0)

-o <outid>: Output run ID (default: msphereX)

--down: Downscale instead of upscale (default: False)

embiggenVOLT

Up/down-scales a Volt restart

inid/nres : Run ID string and restart number, i.e. input file = inid.MPISTUFF.Res.#nres.h5 outid : Output Run ID

usage: embiggenVOLT [-h] [-i inid] [-n nres] [-o outid] [--down]

-h, --help: show this help message and exit

-i <inid>: Input Run ID string (default: msphere)

-n <nres>: Restart number (default: 0)

-o <outid>: Output run ID (default: msphereX)

--down: Downscale instead of upscale (default: False)

genmpiXDMF

Creates series of XMF files from MPI-decomposed Gamera run

usage: genmpiXDMF [-h] [-d directory] [-id runid] [-outid outid] [-sS stride]
                  [--printVars]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: RunID of data (default: msphere)

-outid <outid>: RunID of output XMF files (default: sim)

-sS <stride>: Output cadence (default: 1)

--printVars: Print root and step vars (default: False)

genXDMF

Generates XDMF file from non-MPI HDF5 output

usage: genXDMF [-h] [-outname OUTNAME]
               [-preset {mhdrcm_eq,gam,mhdrcm_bmin,voltSG}] [-rcmf RCMF]
               [-rcmv RCMV] [-rcmk RCMK] [--printVars]
               model.h5

model.h5: Filename of Kaiju HDF5 Output

-h, --help: show this help message and exit

-outname <outname>: Name of generated XMF file

-preset {mhdrcm_eq,gam,mhdrcm_bmin,voltSG}: Tell the script what the file is (in case not derivble from name)

-rcmf <rcmf>: rcm.h5 file to use with ‘-rcmv’ and ‘-rcmk’ args (default: msphere.rcm.h5)

-rcmv <rcmv>: Comma-separated rcm.h5 vars to include in an mhdrcm preset (ex: rcmvm, rcmeeta)

-rcmk <rcmk>: Comma-separated RCM k values to pull from 3D vars specified with ‘-rcmv’

--printVars: Print root and step vars (default: False)

genXLine

Generates XDMF file from CHIMP tracer HDF5 output

usage: genXLine [-h] [-noatts] tracer.h5

tracer.h5: Filename of CHIMP tracer HDF5 Output

-h, --help: show this help message and exit

-noatts: Don’t add XDMF scalars (default: False)

numSteps

Identifies the domain (in steps and time) of a Kaiju HDF-5 file

usage: numSteps [-h] Gamera.h5 [Gamera.h5 ...]

gamera.h5: Filename of Gamera HDF5 Output

-h, --help: show this help message and exit

pitmerge

Joins blocks created by calcdb.x (or similar CHIMP routines) into single file

runid : Run ID

usage: pitmerge [-h] [-runid runid] [-typeid typeid] [--link]

-h, --help: show this help message and exit

-runid <runid>: Input run ID (default: msphere)

-typeid <typeid>: Input type ID (default: deltab)

--link: Create links to existing files rather than copy data (default: False)

printResTimes

Overengineered script to print the time of each restart file by parsing h5dump output

usage: printResTimes [-h] [-id runid] [-f timeFmt] [-ut]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-f <timefmt>: Time format [s,m,h] (default: m)

-ut: Print UT instead of simulation time (default: False)

run_calcdb

Run calcdb.x to compute ground delta-B values.

usage: run_calcdb [-h] [--calcdb CALCDB] [--debug] [--dt DT]
                  [--hpc {derecho,pleiades}] [--parintime PARINTIME]
                  [--pbs_account PBS_ACCOUNT] [--verbose]
                  mage_results_path

mage_results_path: Path to a result file for a MAGE magnetosphere run.

-h, --help: show this help message and exit

--calcdb <calcdb>: Path to calcdb.x binary (default: calcdb.x).

--debug, -d: Print debugging output (default: False).

--dt <dt>: Time interval for delta B computation (simulated seconds) (default: 60.0).

--hpc {derecho,pleiades}: HPC system to run analysis (default: pleiades).

--parintime <parintime>: Split the calculation into this many parallel chunks of kaiju simulation steps, one chunk per node (default: 1).

--pbs_account <pbs_account>: PBS account to use for job accounting (default: None).

--verbose, -v: Print verbose output (default: False).

run_ground_deltaB_analysis

Compare MAGE ground delta-B to SuperMag measurements, and create SuperMAGE analysis maps.

usage: run_ground_deltaB_analysis [-h] [--calcdb CALCDB] [--debug] [--dt DT]
                                  [--hpc {derecho,pleiades}]
                                  [--parintime PARINTIME]
                                  [--pbs_account PBS_ACCOUNT]
                                  [--smuser SMUSER] [--verbose]
                                  mage_results_path

mage_results_path: Path to a result file for a MAGE magnetosphere run.

-h, --help: show this help message and exit

--calcdb <calcdb>: Path to calcdb.x binary (default: calcdb.x).

--debug, -d: Print debugging output (default: False).

--dt <dt>: Time interval for delta-B computation (seconds) (default: 60.0).

--hpc {derecho,pleiades}: HPC system to run analysis (default: pleiades).

--parintime <parintime>: Split the calculation into this many parallel chunks of MAGE simulation steps, one chunk per node (default: 1).

--pbs_account <pbs_account>: PBS account to use for job accounting (default: None).

--smuser <smuser>: Account name for SuperMag database access (default: None).

--verbose, -v: Print verbose output (default: False).

slimFL

Slims down a FL file

usage: slimFL [-h] [-pskip pskip] [-flskip flskip] Fat.h5 Slim.h5

fat.h5: Filename of input fat HDF5 file

slim.h5: Filename of slimmed HDF5 file

-h, --help: show this help message and exit

-pskip <pskip>: Stride over points on field line

-flskip <flskip>: Stride over field lines

slimh5

Slims down an HDF output file

usage: slimh5 [-h] [-s start] [-e end] [-sk nsk] [-sf nsf] [-mpi ijk] [--p]
              Fat.h5 Slim.h5

fat.h5: Filename of input fat HDF5 file

slim.h5: Filename of slimmed HDF5 file

-h, --help: show this help message and exit

-s <start>: Starting slice

-e <end>: Ending slice (default: N)

-sk <nsk>: Stride (default: 1)

-sf <nsf>: File write stride (default: 250)

-mpi <ijk>: Comma-separated mpi dimensions (example: ‘4,4,1’, default: noMPI)

--p: Preserve Step # instead of labeling at Step#0

slimh5_classic

Slims down an HDF output file

usage: slimh5_classic [-h] [-intag intag] [-outtag outtag] [-type type]
                      [-s start] [-e end] [-sk nsk] [-mpi ijk]

-h, --help: show this help message and exit

-intag <intag>: Run ID of input fat HDF file (default: msphere)

-outtag <outtag>: Run ID of output slimmed HDF file (default: slim)

-type <type>: Model type (default: gam)

-s <start>: Starting slice

-e <end>: Ending slice (default: N)

-sk <nsk>: Stride (default: 1)

-mpi <ijk>: Comma-separated mpi dimensions (example: ‘4,4,1’, default: noMPI)

supermag_comparison

Create MAGE-SuperMag comparison plots.

usage: supermag_comparison [-h] [--debug] [--smuser SMUSER] [--verbose]
                           calcdb_results_path

calcdb_results_path: Path to a (possibly merged) result file from calcdb.x.

-h, --help: show this help message and exit

--debug, -d: Print debugging output (default: False).

--smuser <smuser>: SuperMag user ID to use for SuperMag queries (default: ).

--verbose, -v: Print verbose output (default: False).

supermage_analysis

Create SuperMAGE analysis plots.

usage: supermage_analysis [-h] [--debug] [--verbose] mage_results_path

mage_results_path: Path to a MAGE result file.

-h, --help: show this help message and exit

--debug, -d: Print debugging output (default: False).

--verbose, -v: Print verbose output (default: False).

ut2mjd

Returns MJD (modified Julian date) from a given UT UT: UT string, yyyy-mm-ddThh:mm:ss format ut2mjd.py 2010-02-05T5:00:00

usage: ut2mjd [-h] UT

ut: UT string to convert (default: 2010-01-01T00:00:00)

-h, --help: show this help message and exit

Datamodel

The datamodel directory scripts are:

msphParallelSatComp

Extracts information from satellite trajectory for various spacecraft. Spacecraft data is pulled from CDAWeb. Output CDF files contain data pulled from CDAWeb along with data extracted from GAMERA. Image files of satellite comparisons are also produced.

usage: msphParallelSatComp [-h] [-id runid] [-path path] [-cmd command]
                           [-numSeg Number of segments] [--keep]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-path <path>: Path to directory containing REMIX files (default: .)

-cmd <command>: Full path to sctrack.x command

-numSeg <number of segments>: Number of segments to simultaneously process

--keep: Keep intermediate files

msphPbsSatComp

Checks the run for satellites with data available and sets up PBS job scripts for running interpolation in parallel.

usage: msphPbsSatComp [-h] [-id runid] [-path path] [-satId Satellite Id]
                      [-cmd command] [-acct acct] [--keep]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-path <path>: Path to directory containing files (default: .)

-satId <satellite id>: Name of Satellite to compare

-cmd <command>: Full path to sctrack.x command

-acct <acct>: Account number to use in PBS script

--keep: Keep intermediate files

msphSatComp

Extracts information from satellite trajectory for various spacecraft. Space craft data is pulled from CDAWeb. Output CDF files contain data pulled from CDAWeb along with data extracted from GAMERA. Image files of satellite comparisons are also produced.

usage: msphSatComp [-h] [-id runid] [-path path] [-cmd command]
                   [-satId Satellite Id] [-numSeg Number of segments] [--keep]

-h, --help: show this help message and exit

-id <runid>: RunID of data (default: msphere)

-path <path>: Path to directory containing REMIX files (default: .)

-cmd <command>: Full path to sctrack.x command

-satId <satellite id>: Name of Satellite to compare

-numSeg <number of segments>: Number of segments to simulateously process

--keep: Keep intermediate files

rbspSCcomp

Pulls RBSP data and compares it to synthetic RBSP intensity measurementsfrom the simulation, calculated from extracted RBSP trajectory and PSD files.

usage: rbspSCcomp [-h] [-d directory] [-id runid] [-k energy] [-trj scTrk]
                  [-sc spacecraft] [-r0 R0]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: RunID of model data (default: eRBpsd.ps.h5)

-k <energy>: Energy to comparen 1D profile [keV] (default: 1000)

-trj <sctrk>: spacecraft trajectory file (default: RBSP-A_MAGNETOMETER_1SEC-GSM_EMFISIS-L3.sc.h5)

-sc <spacecraft>: RBSP s/c to plot ‘A’ or ‘B’ (default: A)

-r0 <r0>: radius w/in which to mask observations (default: 2.0)

OHelio

The OHelio directory scripts are:

ih2oh

Process configuration file for inner helio to outer helio conversion.

usage: ih2oh [-h] ConfigFileName

configfilename: The name of the configuration file to use (default: startup.config)

-h, --help: show this help message and exit

Raiju

Raiju directory scripts are:

raijudst

Creates series of XMF files from MPI-decomposed Gamera run

usage: raijudst [-h] [-d directory] [-id runid] [-mr runid] [-rmax Re]
                [--nomr]

-h, --help: show this help message and exit

-d <directory>: Directory to read from (default: .)

-id <runid>: RunID of raiju h5 (default: raijuOWD)

-mr <runid>: RunID of mhdrcm h5 (default: msphere)

-rmax <re>: Maximum Req value to eval DPSDst out to (default: 6)

--nomr: Don’t do mhdrcm stuff (default: False)

raijum2m

Do some diagnostics for mapping MHD moments to etas and back.

usage: raijum2m [-h] [-d directory] [-id runid] [-uts %Y-%m-%dT%H:%M:%S]
                [-ute %Y-%m-%dT%H:%M:%S] [-dt stride] [-phi0 int]
                [-mode {summary,step,point}] [-v]

-h, --help: show this help message and exit

-d <directory>: Directory containing data to read (default: /home/docs/checkouts/readthedocs.org/user_builds/kaipy-docs/checkouts/latest/docs/source)

-id <runid>: Run ID of data (default: msphere)

-uts <%y-%m-%dt%h:%m:%s>: First UT (default: -1)

-ute <%y-%m-%dt%h:%m:%s>: Last UT (default: -1)

-dt <stride>: Step stride (in minutes) (default: 10)

-phi0 <int>: Phi value [deg] to probe in ‘point’ mode (default: 180)

-mode {summary,step,point}: What do you wanna do? (default: summary).

-v, --verbose: Print verbose output (default: False).