12345678901234567890123456789012345678901234567890123456789012345678901234567890

* README for the GAMIT/GLOBK test installation
*   Last updated by M. Floyd 200309 21:53 UTC

This example serves the dual purpose of testing your installation and guiding a
new user through the basic steps to get time series and velocities from
GAMIT/GLOBK processing. In the latter sense, it replaces the southern California
example from earlier releases in order to add GNSS other than GPS. If you are an
experienced user, you may want to simply execute the batch file "runtest" to
complete all steps without intervention in about 90 minutes. In fact, running
just one day or one GNSS for 2018 will likely confirm a correct installation. If
you are a novice, however, we strongly recommend that you read this file
thoroughly, execute each of the commands manually and peruse the results until
you understand what that step accomplished. As noted in the installation README,
you will need to download otl_FES2004.grid to a GRIDS/ directory at the same
level as your master installation or edit the sestbl. to omit ocean tidal
loading.

The example is set up to: (1) download RINEX 3 files from CDDIS for ten
continuous stations in Europe and environs for three days in 2016, 2017, and
2018 (note that if long names were used for the RINEX 3 files, they will be
renamed to the older short-names as part of the download); (2) conduct phase
processing (sh_gamit) for GPS-only or GPS, GLONASS, Galileo and Beidou; (3)
compute and plot daily repeatabilities (sh_glred) for each year and combine the
daily h-files (.glx) into a single H-file for each year (.GLX); and (4) compute
repeatabilities and velocities for the three years together (globk/glorg). The
only input file provided in the example is sites.defaults, which is always
specific to the network one is processing. All of the others are copied or
linked from gg/tables and will work for most networks.
 
The structure established by this test of the installation has three GAMIT
processing directories, named (arbitrarily) by year (2014/, 2016/, 2018/), each
of which has below it a rinex/, tables/ and gsoln/ directory specific to that
year. At the top level there is a processing directory (vsoln/) and a tables/
directory for the multi-year GLOBK solution. The steps described assume that you
have downloaded ocean tidal loading grid (e.g. otl_FES2004.grid) to a gg/GRIDS/
directory ("mkdir ~/gg/GRIDS" if it doesn't exist already) and have internet
access while processing; if you do not have these, see Notes 3 and 4 below. In
directory check_files/ are saved copies of the q-files and .org files for each
day, and the .org files and PostScript files for the multi-year repeatablities
and velocities.

Before you start, make sure that you have constructed the paths and aliases
described in the installation README. The example may be run from any directory
on your system, preferably the place you intend to process your own data, not
under gg.

STEP 1: Run GAMIT for three days from 2018

In the test_install/2018/ directory type

  sh_setup -yr 2018

The 2018/tables/ directory will now contain links to most standard files in
gg/tables/ and copies of these files for process.defaults, sestbl., station.info
(complete MIT version), and autcln.cmd. The sites.defaults file was written for
this test (ordinarily one would construct this station list) and already in the
directory, and therefore not overwritten by sh_setup.

Examine tables/sites.defaults to note that it has been set up to download from a
remote archive (CDDIS by default) RINEX files for ten IGS stations and "xstinfo"
is set to avoid any automatic update of station.info during processing. Note
also that the sittbl. copied from gg/tables/ is set up to impose moderate
constraints on IGS core stations to support ambiguity resolution in GAMIT; the
four included in test_install are more than sufficient.

Edit tables/process.defaults to change the "mailto" to your own email address to
receive the sh_gamit summary file. (If left null, it reverts to "whoami", so
this change may not be needed.) Note that "aprf", used to initialize the lfile.
for GAMIT points to igs14_comb.apr, which has been copied by sh_setup to the
2018/tables/ directory.

If you have not downloaded or copied from an earlier distribution the (large)
grid file for ocean tidal loading and do not wish to use it, change "Tides
applied" in tables/sestbl. from "31" to "23".

Construct a small, experiment-specific station.info file by using the following
procedure in the 2018/tables directory:

  sh_upd_stnfo -l sd

will create "station.info.new", using from the MIT station.info only the sites
listed in sites.defaults. (This step will take a while since the MIT global
station.info file is so long.) After checking, rename it to "station.info"
(overwriting the no-longer-useful MIT station.info). (In your own processing, if
you have stations that are not in the MIT station.info file, you can add their
entries from the RINEX headers by running in tables/
"sh_upd_stnfo -files ../rinex/*.18o". (See Section 2.4 of the Intro manual for
what to do if the RINEX header entries are non-standard.)

GAMIT currently supports processing of each GNSS separately, with the day
directories for each created with a single-letter added to designate the system,
e.g. 095G, 095R, 095E, 095C. If you wish to test full GNSS capability, type at
the 2018/ level

  sh_gamit -expt eura -gnss G -s 2018 095 097 -pres ELEV -orbit igsf -copt x k p -dopts c ao >& sh_gamit_2018G.log
  sh_gamit -expt eura -gnss R -s 2018 095 097 -jclock sp3 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2018R.log
  sh_gamit -expt eura -gnss E -s 2018 095 097 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2018E.log
  sh_gamit -expt eura -gnss C -s 2018 095 097 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2018C.log

For GPS-only, omit the -gnss so that the day directory names will be the day-of-
year only.

A summary file should be emailed to you as each day completes execution. Check
these files for number of stations (6), Postfit RMS (3-15 mm, none 0), postfit
nrms (~0.2), ambiguity resolution and coordinate adjustments (< 30 cm). For
this large network, the 2018 ambiguity resolution is 80-90% for GPS and Galileo,
40-50% for Beidou, but near zero for GLONASS due to poor orbits), a condition
also reflected in the sky plots in the figs/ directory. Allowing the GLONASS
orbits to adjust (RELAX mode in the sestbl.) will improve the fit signficantly.
To view the result of the fit of GAMIT's orbit model to the input orbit, see the
rms files in igs/. To view the complete editing statistics see autcln.prefit.sum
and autcln.post.sum in the day directories; for the least-squares adjustment,
see qeuraa.[ddd].

Optionally, remove the x, k, and p files from the day directories to save space:

 sh_cleanup -d 2018 095 096 097 -dopts x k p

Notes:

1. For large or complex data sets, the utility sh_get_times can be helpful in
determining the days and session spans to be processed.

2. In creating station.info for your own experiments, it is important to check
it after updating from the RINEX headers unless you are sure these headers are
correct. In processing, the station.info entries always override whatever is in
the RINEX header or the x-files. An alternative way of creating entries for
survey-mode sites is to use interactive program "make_stnfo", then use
sh_up_stnfo to merge this file with the one created from the MIT station.info
file for continuous sites. The survey-mode file will have a shorter form of the
station.info format, but this will be converted when it is merged with the
continuous file, which should be listed as the reference (-ref) in the call to
sh_upd_stnfo.

3. The example is set up to use ocean tidal loading ("Use otl.grid = Y" in the
sestbl.), which requires you to have previously downloaded into gg/GRIDS/ an
OTL file from the anonymous ftp directory on everest.mit.edu and to have verify
this file is linked to gg/tables/otl.grid. The IERS/IGS standard model is
otl_FES2004.grid (730 Mb). You may, however, substitute the smaller (45 Mb)
otl_CSR4.grid, or you may turn off ocean tidal loading by setting
"Tides applied = 23" and "Use otl.grid = N" in the sestbl. (Note that the links
to the other grid and list files (met.grid, met.list, map.grid, etc.) can remain
empty for running the example and for most processing.

4. If you want or need to run the example without having internet access while
running, you can pre-load the RINEX, navigation, and orbit files into the
rinex/, brdc/, and igs/ directories, respectively.


STEP 2: Run GLOBK to get repeatabilities and a combined H-file for the span

At 2018/:

  sh_glred -cmd

to get the globk.cmd and glorg.cmd files copied from gg/tables to 2018/gsoln,
then

  sh_glred -s 2018 095 2018 097 -expt eura -netext G R E C -opt R H G T >& sh_glred.log

The script as commanded will translate the GAMIT ascii h-files in each day
directory to GLOBK binary h-files (.glx) and put them into the glbf/ directory
(H option); create a gdl file for each day listing the h-file, run GLOBK for
each day (G option) using globk.cmd and glorg.cmd; and generate time series
plots (T option using pos files, program tssum and sh_plot_pos).

For this test the globk/glred and glorg command files created in gsoln/ by
"sh_glred -cmd" will work without editing; however, in general there are changes
you may need to make, for example, to define the reference frame with
translation-only rather than tranlsation and rotation, and to change the list of
reference (stabilization) sites.

The daily plots combining the GNSS measurements for each day, may be found in
gsoln/plots_2018_095-2018_097. You can view the *.org files to see what globk
did, paying attention to the stabilization iteration (what sites were removed),
the chi2 increments in the "EXPERIMENT LIST", and the statitics of the
stabilization ("POS STATISTICS"). In your own runs processing many days, it is
convenient to get a quick summary by grep'ing on *.org with "USED" (from the
chi2 list) and "POS STAT".

Next combine the days to get a single H-file for the 3-day span to use for the
multi-year repeatabilities (time series) and velocities.

 sh_glred -s 2018 095 2018 097 -expt eura -netext G R E C -ncomb 3 -globk_cmd_prefix COMB -opt G >& sh_glred_comb.log


STEP 3: Repeat Steps 1 and 2 for 2016 and 2014:

  At 2016/: sh_setup -yr 2016
  At 2016/tables/, edit process.defaults for mailto
  At 2016/tables/: sh_upd_stnfo -l sd ; mv station.info.new station.info
  At 2016/:
   sh_gamit -expt eura -gnss G -s 2016 101 102 -pres ELEV -orbit igsf -copt x k p -dopts c ao >& sh_gamit_2016G.log
   sh_gamit -expt eura -gnss R -s 2016 101 102 -jclock sp3 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2016R.log
   sh_gamit -expt eura -gnss E -s 2016 101 102 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2016E.log
   sh_gamit -expt eura -gnss C -s 2016 101 102 -pres ELEV -orbit codm -copt x k p -dopts c ao >& sh_gamit_2016C.log
   sh_glred -cmd
   sh_glred -s 2016 101 2016 102 -expt eura -opt H G T >& sh_glred_2016.log
   sh_glred -s 2016 101 2016 102 -expt eura -netext G R E C -ncomb 2 -globk_cmd_prefix COMB -opt G >& sh_glred_comb.log

  At 2014/: sh_setup -yr 2014
  At 2014/tables/: edit process.defaults for mailto
  At 2014/tables/: sh_upd_stnfo -l sd ; mv station.info.new station.info
  At 2014/
   sh_gamit -expt eura -gnss G -s 2014 113 114 -pres ELEV -orbit igsf -copt x k p -dopts c ao >& sh_gamit_2014G.log
   sh_gamit -expt eura -gnss R -s 2014 113 114 -jclock sp3 -pres ELEV -orbit comf -copt x k p -dopts c ao >& sh_gamit_2014R.log
   sh_glred -cmd
   sh_glred -s 2014 113 2014 114 -expt eura -opt H G T >& sh_glred_2014.log
   sh_glred -s 2014 113 2014 114 -expt eura -netext G R -ncomb 2 -globk_cmd_prefix COMB -opt G >& sh_glred_comb.log

We've specified only 2 days in 2016 and 2014 to save run time, and we've
included only GPS and GLONASS for 2014 since there were too few Beidou and
Galileo satellites available at that time to obtain an accurate solution.


STEP 4: Run GLOBK to get 3-epoch (4-yr) repeatabilities and velocities

The key user-specific controls for this step (also incorporated in the sh_glred
runs within each year) are the list of sites to be used in defining the
reference frame, and the a priori coordinates for these sites. Here we use the
same sites and coordinate file (igs14_comb.apr) as in the single-year solutions,
but this may not always be the case. For the multi-year repeatabilities, we will
use the combined H-files (.GLX) created in the year gsoln/ directories. So
create a solution directory at the top level

  mkdir vsoln

then cd vsoln and get create a list of combined h-files for globk:

 ls ../????/gsoln/H*GLX > eura.gdl

For large or complex data sets, it's helpful at this point to run glist which
will check for blunders and give you a list of all the sites used and their
spans. Program glist2cmd can then be helpful in establishing a use_site list. It
may also be desirable to aggregate the data within each year, both to save time
in the multi-year combination and to provide more representative long-term
statistics. The procedure for doing this is given in the file sGPS_recipe.txt in
the documentation directory in the ftp area or web site.

 \rm globk_replong.org globk_replong.log
 glred 6 globk_replong.prt globk_replong.log eura.gdl globk.cmd >& glred.out

Unlike in sh_glred, the rm command may be needed here since glred will
concatenate the new log and org files with any previous files of the
same name. The globk_replong.prt will not be created since we have set
"prt_opt NOPR" in globk.cmd.

Create the pos files for plotting:

tssum . mit.final.igs14 -R globk_replong.org

Create the multi-year plots:

sh_plot_pos -f *.pos -r -t NONE -u -t1 2014-001 -t2 2018-180

Get velocities from the 4-year span:

 \rm globk_vel.org globk_vel.log
 globk 6 globk_vel.prt globk_vel.log eura.gdl globk.cmd VEL >& globk.out

where the "VEL" token at the end tells globk to uncomment the lines in globk.cmd
that begin with "VEL".

Check the globk_vel.org file under EXPERIMENT LIST for the chi2 increments
(< 1.0) in stacking the 3 H-files and the stabilization statistics in the "VEL
STATISTICS" and "POS STATISTICS" lines. For this network and the IGS14
(ITRF2014) apr file, the 9 stabilization stations fit the reference frame in
velocity at the level of ~1 mm/yr horizontal and 5 mm/yr vertical with
uncertainties about half of the rms.

Plot the velocities using

 sh_plotvel -ps euratest -f globk_vel.org -R-60/50/-5/55 -factor 0.5 -arrow_value 10 -page L

(Type "sh_plotvel" without arguments to see the full range of options for
producing more attractive maps.)

------------

To start over from scratch, run sh_clean_test, once for each year and once for
the velocity solution. (Type the name of the script without arguments to see the
documentation.)

12345678901234567890123456789012345678901234567890123456789012345678901234567890