SABGOM Access issue - new variables in SABGOM model?

[kwilcox]

I think I've figured out the issue... querying by time used to be the way to pull data, but it appears that the aggregation is now dimensioning some variables using time and others using time1. Were new variables added to the aggregation recently?

The time variable is missing values from 180 to 471 while the time1 variable has those values.

@jbzambon

[rsignell-usgs]

Yep! Looking at the DDS reveals:

    Float32 zeta[time2 = 16131][eta_rho = 320][xi_rho = 440];
    Float32 ubar[time2 = 16131][eta_u = 320][xi_u = 439];
    Float32 vbar[time2 = 16131][eta_v = 319][xi_v = 440];
    Float32 u[time2 = 16131][s_rho = 36][eta_u = 320][xi_u = 439];
    Float32 v[time2 = 16131][s_rho = 36][eta_v = 319][xi_v = 440];
    Float32 w[time2 = 16131][s_w = 37][eta_rho = 320][xi_rho = 440];
    Float32 temp[time2 = 16131][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 salt[time2 = 16131][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 NO3[time = 12076][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 NH4[time = 12076][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 chlorophyll[time1 = 12761][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 phytoplankton[time1 = 12761][s_rho = 36][eta_rho = 320][xi_rho = 440];
    Float32 zooplankton[time1 = 12761][s_rho = 36][eta_rho = 320][xi_rho = 440];

[kwilcox]

http://oceanus.meas.ncsu.edu apparently has 3 time dimensions and not 2 like http://omgsrv1.meas.ncsu.edu. @jbzambon which should I be using to pull in the data?

[rsignell-usgs]

The good news is that netcdf subset does the right thing, if you just specify a time value or time range and you don't to worry about the number of different time variables:

http://oceanus.meas.ncsu.edu:8080/thredds/ncss/fmrc/sabgom_roms/SABGOM_ROMS_Forecast_Model_Run_Collection_best.ncd?var=angle&var=f&var=h&var=mask_psi&var=mask_rho&var=mask_u&var=mask_v&var=pm&var=pn&var=NH4&var=NO3&var=chlorophyll&var=phytoplankton&var=zooplankton&var=ubar&var=vbar&var=zeta&var=salt&var=temp&var=u&var=v&var=w&disableLLSubset=on&disableProjSubset=on&horizStride=1&time=2017-04-02T00%3A00%3A00Z&vertCoord=&addLatLon=true&accept=netcdf4

[kwilcox]

@rsignell-usgs @jbzambon Can you confirm that you are seeing incorrect (changed) _FillValue attributes when downloaded from NCSS?

THREDDS says the _FillValue is NaN (which is correct, the data contains NaN as needed) but when downloading from NCSS the resulting files contain a _FillValue of 0.f.

[kwilcox]

Neverrrmind, the _FillValue attributes are different/incorrect on
http://oceanus.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom_roms/SABGOM_ROMS_Forecast_Model_Run_Collection_best.ncd.html

units: meter second-1
long_name: u-momentum component
time: ocean_time
coordinates: time2_run time2 s_rho lat_u lon_u 
field: u-velocity, scalar, series
_FillValue: 0.0
standard_name: eastward_sea_water_velocity_assuming_no_tide

[jbzambon]

Sorry all, I'm traveling through Monday, I won't be able to get to this until Monday afternoon.

…

-Joe

On Mar 31, 2017, at 12:24 PM, Kyle Wilcox ***@***.***> wrote: Neverrrmind, the _FillValue attributes are different/incorrect on http://oceanus.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom_roms/SABGOM_ROMS_Forecast_Model_Run_Collection_best.ncd.html <http://oceanus.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom_roms/SABGOM_ROMS_Forecast_Model_Run_Collection_best.ncd.html> units: meter second-1 long_name: u-momentum component time: ocean_time coordinates: time2_run time2 s_rho lat_u lon_u field: u-velocity, scalar, series _FillValue: 0.0 standard_name: eastward_sea_water_velocity_assuming_no_tide — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMOXrgiiJzHu4kFy1v9VEZeaKcrcsMJkks5rrSjagaJpZM4Mu6OO>.

[rsignell-usgs]

@kwilcox , I put the 1 step file I downloaded from oceanus via NCSS on my THREDDS Server:
http://geoport-dev.whoi.edu/thredds/dodsC/sand/usgs/users/rsignell/data/sabgom/SABGOM_ROMS_Forecast_Model_Run_Collection_best.ncd.nc.html

Some vars like temp and salt have _FillValue: 0.0 but others like ubar have _FillValue: 1.0E37.

I don't think there is a bug.

Things like Godiva2 appear to work just fine:

[kwilcox]

See #5 (comment). The _FillValue for a bunch of variables is "0.0", but NaNs are in the file. 🤷‍♂️, I've never seen current vectors or temperature with a fill value of 0.0 so was asking if it was correct!

[rsignell-usgs]

We often set the fill value to 0.0 for temp, salt, u, v, zeta, etc for older ROMS runs before they actually wrote a fill value. Otherwise the land was covered with 0.0 values. Figured values of exactly 0.0 were unlikely in realistic model runs.

I'm sure I gave @jbzambon those sample ROMS catalogs or perhaps even created them. Perhaps they could be changed now if using more modern version of ROMS.

[kwilcox]

[kwilcox]

The additional time dimensions have dropped off of the DAP aggregation now and its back to only time: http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom/SABGOM_Forecast_Model_Run_Collection_best.ncd.html. Does newer data not have any of the variables that were dimensioned by those?

[jbzambon]

Yes, there were several iterations of model output as we gained access to more storage. We also recently had to upgrade the version of ROMS as the old one was incompatible with new hardware.

…

-Joe 650M Dec 2 2015 his_20111130.nc 6.9G Apr 5 09:09 his_20170405.nc ************************************************ ncdump -h his_20111130.nc netcdf his_20111130 { dimensions: xi_rho = 440 ; xi_u = 439 ; xi_v = 440 ; xi_psi = 439 ; eta_rho = 320 ; eta_u = 320 ; eta_v = 319 ; eta_psi = 319 ; N = 36 ; s_rho = 36 ; s_w = 37 ; tracer = 2 ; boundary = 4 ; ocean_time = UNLIMITED ; // (8 currently) variables: int ntimes ; ntimes:long_name = "number of long time-steps" ; int ndtfast ; ndtfast:long_name = "number of short time-steps" ; double dt ; dt:long_name = "size of long time-steps" ; dt:units = "second" ; double dtfast ; dtfast:long_name = "size of short time-steps" ; dtfast:units = "second" ; double dstart ; dstart:long_name = "time stamp assigned to model initilization" ; dstart:units = "days since 1858-11-17 00:00:00" ; int nHIS ; nHIS:long_name = "number of time-steps between history records" ; int ndefHIS ; ndefHIS:long_name = "number of time-steps between the creation of history files" ; int nRST ; nRST:long_name = "number of time-steps between restart records" ; nRST:cycle = "only latest two records are maintained" ; int ntsAVG ; ntsAVG:long_name = "starting time-step for accumulation of time-averaged fields" ; int nAVG ; nAVG:long_name = "number of time-steps between time-averaged records" ; int ndefAVG ; ndefAVG:long_name = "number of time-steps between the creation of average files" ; int nSTA ; nSTA:long_name = "number of time-steps between stations records" ; double Falpha ; Falpha:long_name = "Power-law shape barotropic filter parameter" ; double Fbeta ; Fbeta:long_name = "Power-law shape barotropic filter parameter" ; double Fgamma ; Fgamma:long_name = "Power-law shape barotropic filter parameter" ; double nl_tnu2(tracer) ; nl_tnu2:long_name = "nonlinear model Laplacian mixing coefficient for tracers" ; nl_tnu2:units = "meter2 second-1" ; double nl_visc2 ; nl_visc2:long_name = "nonlinear model Laplacian mixing coefficient for momentum" ; nl_visc2:units = "meter2 second-1" ; double Akt_bak(tracer) ; Akt_bak:long_name = "background vertical mixing coefficient for tracers" ; Akt_bak:units = "meter2 second-1" ; double Akv_bak ; Akv_bak:long_name = "background vertical mixing coefficient for momentum" ; Akv_bak:units = "meter2 second-1" ; double Akk_bak ; Akk_bak:long_name = "background vertical mixing coefficient for turbulent energy" ; Akk_bak:units = "meter2 second-1" ; double Akp_bak ; Akp_bak:long_name = "background vertical mixing coefficient for length scale" ; Akp_bak:units = "meter2 second-1" ; double rdrg ; rdrg:long_name = "linear drag coefficient" ; rdrg:units = "meter second-1" ; double rdrg2 ; rdrg2:long_name = "quadratic drag coefficient" ; double Zob ; Zob:long_name = "bottom roughness" ; Zob:units = "meter" ; double Zos ; Zos:long_name = "surface roughness" ; Zos:units = "meter" ; double Znudg ; Znudg:long_name = "free-surface nudging/relaxation inverse time scale" ; Znudg:units = "day-1" ; double M2nudg ; M2nudg:long_name = "2D momentum nudging/relaxation inverse time scale" ; M2nudg:units = "day-1" ; double M3nudg ; M3nudg:long_name = "3D momentum nudging/relaxation inverse time scale" ; M3nudg:units = "day-1" ; double Tnudg(tracer) ; Tnudg:long_name = "Tracers nudging/relaxation inverse time scale" ; Tnudg:units = "day-1" ; double FSobc_in(boundary) ; FSobc_in:long_name = "free-surface inflow, nudging inverse time scale" ; FSobc_in:units = "second-1" ; double FSobc_out(boundary) ; FSobc_out:long_name = "free-surface outflow, nudging inverse time scale" ; FSobc_out:units = "second-1" ; double M2obc_in(boundary) ; M2obc_in:long_name = "2D momentum inflow, nudging inverse time scale" ; M2obc_in:units = "second-1" ; double M2obc_out(boundary) ; M2obc_out:long_name = "2D momentum outflow, nudging inverse time scale" ; M2obc_out:units = "second-1" ; double Tobc_in(boundary, tracer) ; Tobc_in:long_name = "tracers inflow, nudging inverse time scale" ; Tobc_in:units = "second-1" ; double Tobc_out(boundary, tracer) ; Tobc_out:long_name = "tracers outflow, nudging inverse time scale" ; Tobc_out:units = "second-1" ; double M3obc_in(boundary) ; M3obc_in:long_name = "3D momentum inflow, nudging inverse time scale" ; M3obc_in:units = "second-1" ; double M3obc_out(boundary) ; M3obc_out:long_name = "3D momentum outflow, nudging inverse time scale" ; M3obc_out:units = "second-1" ; double rho0 ; rho0:long_name = "mean density used in Boussinesq approximation" ; rho0:units = "kilogram meter-3" ; double gamma2 ; gamma2:long_name = "slipperiness parameter" ; char spherical ; spherical:long_name = "grid type logical switch" ; spherical:flag_values = "T, F" ; spherical:flag_meanings = "spherical Cartesian" ; double xl ; xl:long_name = "domain length in the XI-direction" ; xl:units = "meter" ; double el ; el:long_name = "domain length in the ETA-direction" ; el:units = "meter" ; int Vtransform ; Vtransform:long_name = "vertical terrain-following transformation equation" ; int Vstretching ; Vstretching:long_name = "vertical terrain-following stretching function" ; double theta_s ; theta_s:long_name = "S-coordinate surface control parameter" ; double theta_b ; theta_b:long_name = "S-coordinate bottom control parameter" ; double Tcline ; Tcline:long_name = "S-coordinate surface/bottom layer width" ; Tcline:units = "meter" ; double hc ; hc:long_name = "S-coordinate parameter, critical depth" ; hc:units = "meter" ; double s_rho(s_rho) ; s_rho:long_name = "S-coordinate at RHO-points" ; s_rho:valid_min = -1. ; s_rho:valid_max = 0. ; s_rho:positive = "up" ; s_rho:standard_name = "ocean_s_coordinate_g1" ; s_rho:formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc" ; s_rho:field = "s_rho, scalar" ; double s_w(s_w) ; s_w:long_name = "S-coordinate at W-points" ; s_w:valid_min = -1. ; s_w:valid_max = 0. ; s_w:positive = "up" ; s_w:standard_name = "ocean_s_coordinate_g1" ; s_w:formula_terms = "s: s_w C: Cs_w eta: zeta depth: h depth_c: hc" ; s_w:field = "s_w, scalar" ; double Cs_r(s_rho) ; Cs_r:long_name = "S-coordinate stretching curves at RHO-points" ; Cs_r:valid_min = -1. ; Cs_r:valid_max = 0. ; Cs_r:field = "Cs_r, scalar" ; double Cs_w(s_w) ; Cs_w:long_name = "S-coordinate stretching curves at W-points" ; Cs_w:valid_min = -1. ; Cs_w:valid_max = 0. ; Cs_w:field = "Cs_w, scalar" ; double h(eta_rho, xi_rho) ; h:long_name = "bathymetry at RHO-points" ; h:units = "meter" ; h:coordinates = "lon_rho lat_rho" ; h:field = "bath, scalar" ; double f(eta_rho, xi_rho) ; f:long_name = "Coriolis parameter at RHO-points" ; f:units = "second-1" ; f:coordinates = "lon_rho lat_rho" ; f:field = "coriolis, scalar" ; double pm(eta_rho, xi_rho) ; pm:long_name = "curvilinear coordinate metric in XI" ; pm:units = "meter-1" ; pm:coordinates = "lon_rho lat_rho" ; pm:field = "pm, scalar" ; double pn(eta_rho, xi_rho) ; pn:long_name = "curvilinear coordinate metric in ETA" ; pn:units = "meter-1" ; pn:coordinates = "lon_rho lat_rho" ; pn:field = "pn, scalar" ; double lon_rho(eta_rho, xi_rho) ; lon_rho:long_name = "longitude of RHO-points" ; lon_rho:units = "degree_east" ; lon_rho:standard_name = "longitude" ; lon_rho:field = "lon_rho, scalar" ; double lat_rho(eta_rho, xi_rho) ; lat_rho:long_name = "latitude of RHO-points" ; lat_rho:units = "degree_north" ; lat_rho:standard_name = "latitude" ; lat_rho:field = "lat_rho, scalar" ; double lon_u(eta_u, xi_u) ; lon_u:long_name = "longitude of U-points" ; lon_u:units = "degree_east" ; lon_u:standard_name = "longitude" ; lon_u:field = "lon_u, scalar" ; double lat_u(eta_u, xi_u) ; lat_u:long_name = "latitude of U-points" ; lat_u:units = "degree_north" ; lat_u:standard_name = "latitude" ; lat_u:field = "lat_u, scalar" ; double lon_v(eta_v, xi_v) ; lon_v:long_name = "longitude of V-points" ; lon_v:units = "degree_east" ; lon_v:standard_name = "longitude" ; lon_v:field = "lon_v, scalar" ; double lat_v(eta_v, xi_v) ; lat_v:long_name = "latitude of V-points" ; lat_v:units = "degree_north" ; lat_v:standard_name = "latitude" ; lat_v:field = "lat_v, scalar" ; double lon_psi(eta_psi, xi_psi) ; lon_psi:long_name = "longitude of PSI-points" ; lon_psi:units = "degree_east" ; lon_psi:standard_name = "longitude" ; lon_psi:field = "lon_psi, scalar" ; double lat_psi(eta_psi, xi_psi) ; lat_psi:long_name = "latitude of PSI-points" ; lat_psi:units = "degree_north" ; lat_psi:standard_name = "latitude" ; lat_psi:field = "lat_psi, scalar" ; double angle(eta_rho, xi_rho) ; angle:long_name = "angle between XI-axis and EAST" ; angle:units = "radians" ; angle:coordinates = "lon_rho lat_rho" ; angle:field = "angle, scalar" ; double mask_rho(eta_rho, xi_rho) ; mask_rho:long_name = "mask on RHO-points" ; mask_rho:flag_values = 0., 1. ; mask_rho:flag_meanings = "land water" ; mask_rho:coordinates = "lon_rho lat_rho" ; double mask_u(eta_u, xi_u) ; mask_u:long_name = "mask on U-points" ; mask_u:flag_values = 0., 1. ; mask_u:flag_meanings = "land water" ; mask_u:coordinates = "lon_u lat_u" ; double mask_v(eta_v, xi_v) ; mask_v:long_name = "mask on V-points" ; mask_v:flag_values = 0., 1. ; mask_v:flag_meanings = "land water" ; mask_v:coordinates = "lon_v lat_v" ; double mask_psi(eta_psi, xi_psi) ; mask_psi:long_name = "mask on psi-points" ; mask_psi:flag_values = 0., 1. ; mask_psi:flag_meanings = "land water" ; mask_psi:coordinates = "lon_psi lat_psi" ; double ocean_time(ocean_time) ; ocean_time:long_name = "time since initialization" ; ocean_time:units = "seconds since 1858-11-17 00:00:00" ; ocean_time:calendar = "gregorian" ; ocean_time:field = "time, scalar, series" ; float zeta(ocean_time, eta_rho, xi_rho) ; zeta:long_name = "free-surface" ; zeta:units = "meter" ; zeta:time = "ocean_time" ; zeta:coordinates = "lon_rho lat_rho ocean_time" ; zeta:field = "free-surface, scalar, series" ; zeta:_FillValue = 1.e+37f ; float ubar(ocean_time, eta_u, xi_u) ; ubar:long_name = "vertically integrated u-momentum component" ; ubar:units = "meter second-1" ; ubar:time = "ocean_time" ; ubar:coordinates = "lon_u lat_u ocean_time" ; ubar:field = "ubar-velocity, scalar, series" ; ubar:_FillValue = 1.e+37f ; float vbar(ocean_time, eta_v, xi_v) ; vbar:long_name = "vertically integrated v-momentum component" ; vbar:units = "meter second-1" ; vbar:time = "ocean_time" ; vbar:coordinates = "lon_v lat_v ocean_time" ; vbar:field = "vbar-velocity, scalar, series" ; vbar:_FillValue = 1.e+37f ; float u(ocean_time, s_rho, eta_u, xi_u) ; u:long_name = "u-momentum component" ; u:units = "meter second-1" ; u:time = "ocean_time" ; u:coordinates = "lon_u lat_u s_rho ocean_time" ; u:field = "u-velocity, scalar, series" ; u:_FillValue = 1.e+37f ; float v(ocean_time, s_rho, eta_v, xi_v) ; v:long_name = "v-momentum component" ; v:units = "meter second-1" ; v:time = "ocean_time" ; v:coordinates = "lon_v lat_v s_rho ocean_time" ; v:field = "v-velocity, scalar, series" ; v:_FillValue = 1.e+37f ; float temp(ocean_time, s_rho, eta_rho, xi_rho) ; temp:long_name = "potential temperature" ; temp:units = "Celsius" ; temp:time = "ocean_time" ; temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ; temp:field = "temperature, scalar, series" ; temp:_FillValue = 1.e+37f ; float salt(ocean_time, s_rho, eta_rho, xi_rho) ; salt:long_name = "salinity" ; salt:time = "ocean_time" ; salt:coordinates = "lon_rho lat_rho s_rho ocean_time" ; salt:field = "salinity, scalar, series" ; salt:_FillValue = 1.e+37f ; // global attributes: :file = "/share2/omg/SABGOM_2011/sabgom_his_0335.nc" ; :format = "netCDF-3 classic file" ; :Conventions = "CF-1.0" ; :type = "ROMS/TOMS history file" ; :title = "ROMS/TOMS 3.4 - South-Atlantic Bight and Gulf of Mexico" ; :rst_file = "/share2/omg/SABGOM_2011/sabgom_rst.nc" ; :his_base = "/share2/omg/SABGOM_2011/sabgom_his" ; :avg_file = "/share2/omg/SABGOM_2011/sabgom_avg.nc" ; :sta_file = "/share2/omg/SABGOM_2011/sabgom_sta.nc" ; :flt_file = "/share2/omg/SABGOM_2011/sabgom_flt.nc" ; :grd_file = "/he_data/he/zxue/Projects/SABGOM_2011/sabgom_grd_H.nc" ; :ini_file = "/he_data/he/zxue/Projects/SABGOM_2011/In/sabgom_ini_20101231.nc" ; :frc_file_01 = "./In/FRC/cloud_11_sabgom_fix.nc" ; :frc_file_02 = "./In/FRC/Pair_11_sabgom_fix.nc" ; :frc_file_03 = "./In/FRC/Qair_11_sabgom_fix.nc" ; :frc_file_04 = "./In/FRC/rain_11_sabgom_fix.nc" ; :frc_file_05 = "./In/FRC/swrad_11_sabgom_fix.nc" ; :frc_file_06 = "./In/FRC/Tair_11_sabgom_fix.nc" ; :frc_file_07 = "./In/FRC/lwrad_11_sabgom_fix.nc" ; :frc_file_08 = "./In/FRC/Uwind_11_sabgom_fix.nc" ; :frc_file_09 = "./In/FRC/Vwind_11_sabgom_fix.nc" ; :frc_file_10 = "/he_data/he/zxue/Projects/SABGOM_BIO/sabgom_tide.nc" ; :frc_file_11 = "/he_data/he/hyun/bpspill/in/sabgom_river_7_salt_5.nc" ; :bry_file = "/he_data/he/zxue/Projects/SABGOM_2011/In/sabgom_bc_ncoda.nc" ; :clm_file = "/he_data/he/zxue/Projects/SABGOM_2011/In/sabgom_clm_ncoda.nc" ; :script_file = "./ocean_sabgom.in" ; :fpos_file = "/he_data/he/hyun/bpspill/expt_02.1/floats_oil.in" ; :spos_file = "/he_data/he/hyun/autosabgom/in/stations_sabgom.in" ; :svn_url = "https://www.myroms.org/svn/src/trunk" ; :svn_rev = "412M" ; :code_dir = "/he_data/he/zxue/COAWST411" ; :header_dir = "/he_data/he/zxue/Projects/SABGOM_2011" ; :header_file = "sabgom.h" ; :os = "Linux" ; :cpu = "x86_64" ; :compiler_system = "pgi" ; :compiler_command = "/usr/local/apps/mpich/x86_64/pgi105/mx127..7/bin/mpif90" ; :compiler_flags = "-fastsse -Kieee -fastsse -Mipa=fast -tp k8-64 -Mfree" ; :tiling = "008x007" ; :history = "ROMS/TOMS, Version 3.4, Monday - February 6, 2012 - 10:54:11 AM" ; :ana_file = "ROMS/Functionals/ana_btflux.h, ROMS/Functionals/ana_nudgcoef.h" ; :CPP_options = "SABGOM, ADD_FSOBC, ADD_M2OBC, ANA_BSFLUX, ANA_BTFLUX, ASSUMED_SHAPE, AVERAGES, BULK_FLUXES, CURVGRID, DJ_GRADPS, DOUBLE_PRECISION, EAST_FSCHAPMAN, EAST_M2FLATHER, EAST_M3NUDGING, EAST_M3RADIATION, EAST_TNUDGING, EAST_TRADIATION, EMINUSP, FLOATS, KANTHA_CLAYSON, MASKING, MIX_GEO_TS, MIX_S_UV, MPI, MY25_MIXING, NONLINEAR, NONLIN_EOS, NORTHERN_WALL, N2S2_HORAVG, POWER_LAW, PROFILE, K_C4ADVECTION, RADIATION_2D, !RST_SINGLE, SALINITY, SOLAR_SOURCE, SOLVE3D, SOUTH_FSCHAPMAN, SOUTH_M2FLATHER, SOUTH_M3NUDGING, SOUTH_M3RADIATION, SOUTH_TNUDGING, SOUTH_TRADIATION, SPLINES, SSH_TIDES, STATIONS, TCLIMATOLOGY, TCLM_NUDGING, TS_U3HADVECTION, TS_C4VADVECTION, TS_DIF2, UV_ADV, UV_COR, UV_U3HADVECTION, UV_C4VADVECTION, UV_QDRAG, UV_TIDES, UV_VIS2, VAR_RHO_2D, WESTERN_WALL" ; } ************************************************ ************************************************ ncdump -h his_20170405.nc netcdf his_20170405 { dimensions: xi_rho = 440 ; xi_u = 439 ; xi_v = 440 ; xi_psi = 439 ; eta_rho = 320 ; eta_u = 320 ; eta_v = 319 ; eta_psi = 319 ; N = 36 ; s_rho = 36 ; s_w = 37 ; tracer = 14 ; boundary = 4 ; ocean_time = UNLIMITED ; // (36 currently) variables: int ntimes ; ntimes:long_name = "number of long time-steps" ; int ndtfast ; ndtfast:long_name = "number of short time-steps" ; double dt ; dt:long_name = "size of long time-steps" ; dt:units = "second" ; double dtfast ; dtfast:long_name = "size of short time-steps" ; dtfast:units = "second" ; double dstart ; dstart:long_name = "time stamp assigned to model initilization" ; dstart:units = "days since 1858-11-17 00:00:00" ; int nHIS ; nHIS:long_name = "number of time-steps between history records" ; int ndefHIS ; ndefHIS:long_name = "number of time-steps between the creation of history files" ; int nRST ; nRST:long_name = "number of time-steps between restart records" ; nRST:cycle = "only latest two records are maintained" ; int ntsDIA ; ntsDIA:long_name = "starting time-step for accumulation of diagnostic fields" ; int nDIA ; nDIA:long_name = "number of time-steps between diagnostic records" ; int ndefDIA ; ndefDIA:long_name = "number of time-steps between the creation of diagnostic files" ; int nSTA ; nSTA:long_name = "number of time-steps between stations records" ; double Falpha ; Falpha:long_name = "Power-law shape barotropic filter parameter" ; double Fbeta ; Fbeta:long_name = "Power-law shape barotropic filter parameter" ; double Fgamma ; Fgamma:long_name = "Power-law shape barotropic filter parameter" ; double nl_tnu2(tracer) ; nl_tnu2:long_name = "nonlinear model Laplacian mixing coefficient for tracers" ; nl_tnu2:units = "meter2 second-1" ; double nl_visc2 ; nl_visc2:long_name = "nonlinear model Laplacian mixing coefficient for momentum" ; nl_visc2:units = "meter2 second-1" ; int LuvSponge ; LuvSponge:long_name = "horizontal viscosity sponge activation switch" ; LuvSponge:flag_values = 0, 1 ; LuvSponge:flag_meanings = ".FALSE. .TRUE." ; int LtracerSponge(tracer) ; LtracerSponge:long_name = "horizontal diffusivity sponge activation switch" ; LtracerSponge:flag_values = 0, 1 ; LtracerSponge:flag_meanings = ".FALSE. .TRUE." ; double Akt_bak(tracer) ; Akt_bak:long_name = "background vertical mixing coefficient for tracers" ; Akt_bak:units = "meter2 second-1" ; double Akv_bak ; Akv_bak:long_name = "background vertical mixing coefficient for momentum" ; Akv_bak:units = "meter2 second-1" ; double Akk_bak ; Akk_bak:long_name = "background vertical mixing coefficient for turbulent energy" ; Akk_bak:units = "meter2 second-1" ; double Akp_bak ; Akp_bak:long_name = "background vertical mixing coefficient for length scale" ; Akp_bak:units = "meter2 second-1" ; double rdrg ; rdrg:long_name = "linear drag coefficient" ; rdrg:units = "meter second-1" ; double rdrg2 ; rdrg2:long_name = "quadratic drag coefficient" ; double Zob ; Zob:long_name = "bottom roughness" ; Zob:units = "meter" ; double Zos ; Zos:long_name = "surface roughness" ; Zos:units = "meter" ; double Znudg ; Znudg:long_name = "free-surface nudging/relaxation inverse time scale" ; Znudg:units = "day-1" ; double M2nudg ; M2nudg:long_name = "2D momentum nudging/relaxation inverse time scale" ; M2nudg:units = "day-1" ; double M3nudg ; M3nudg:long_name = "3D momentum nudging/relaxation inverse time scale" ; M3nudg:units = "day-1" ; double Tnudg(tracer) ; Tnudg:long_name = "Tracers nudging/relaxation inverse time scale" ; Tnudg:units = "day-1" ; double FSobc_in(boundary) ; FSobc_in:long_name = "free-surface inflow, nudging inverse time scale" ; FSobc_in:units = "second-1" ; double FSobc_out(boundary) ; FSobc_out:long_name = "free-surface outflow, nudging inverse time scale" ; FSobc_out:units = "second-1" ; double M2obc_in(boundary) ; M2obc_in:long_name = "2D momentum inflow, nudging inverse time scale" ; M2obc_in:units = "second-1" ; double M2obc_out(boundary) ; M2obc_out:long_name = "2D momentum outflow, nudging inverse time scale" ; M2obc_out:units = "second-1" ; double Tobc_in(boundary, tracer) ; Tobc_in:long_name = "tracers inflow, nudging inverse time scale" ; Tobc_in:units = "second-1" ; double Tobc_out(boundary, tracer) ; Tobc_out:long_name = "tracers outflow, nudging inverse time scale" ; Tobc_out:units = "second-1" ; double M3obc_in(boundary) ; M3obc_in:long_name = "3D momentum inflow, nudging inverse time scale" ; M3obc_in:units = "second-1" ; double M3obc_out(boundary) ; M3obc_out:long_name = "3D momentum outflow, nudging inverse time scale" ; M3obc_out:units = "second-1" ; double rho0 ; rho0:long_name = "mean density used in Boussinesq approximation" ; rho0:units = "kilogram meter-3" ; double gamma2 ; gamma2:long_name = "slipperiness parameter" ; int LuvSrc ; LuvSrc:long_name = "momentum point sources and sink activation switch" ; LuvSrc:flag_values = 0, 1 ; LuvSrc:flag_meanings = ".FALSE. .TRUE." ; int LwSrc ; LwSrc:long_name = "mass point sources and sink activation switch" ; LwSrc:flag_values = 0, 1 ; LwSrc:flag_meanings = ".FALSE. .TRUE." ; int LtracerSrc(tracer) ; LtracerSrc:long_name = "tracer point sources and sink activation switch" ; LtracerSrc:flag_values = 0, 1 ; LtracerSrc:flag_meanings = ".FALSE. .TRUE." ; int LsshCLM ; LsshCLM:long_name = "sea surface height climatology processing switch" ; LsshCLM:flag_values = 0, 1 ; LsshCLM:flag_meanings = ".FALSE. .TRUE." ; int Lm2CLM ; Lm2CLM:long_name = "2D momentum climatology processing switch" ; Lm2CLM:flag_values = 0, 1 ; Lm2CLM:flag_meanings = ".FALSE. .TRUE." ; int Lm3CLM ; Lm3CLM:long_name = "3D momentum climatology processing switch" ; Lm3CLM:flag_values = 0, 1 ; Lm3CLM:flag_meanings = ".FALSE. .TRUE." ; int LtracerCLM(tracer) ; LtracerCLM:long_name = "tracer climatology processing switch" ; LtracerCLM:flag_values = 0, 1 ; LtracerCLM:flag_meanings = ".FALSE. .TRUE." ; int LnudgeM2CLM ; LnudgeM2CLM:long_name = "2D momentum climatology nudging activation switch" ; LnudgeM2CLM:flag_values = 0, 1 ; LnudgeM2CLM:flag_meanings = ".FALSE. .TRUE." ; int LnudgeM3CLM ; LnudgeM3CLM:long_name = "3D momentum climatology nudging activation switch" ; LnudgeM3CLM:flag_values = 0, 1 ; LnudgeM3CLM:flag_meanings = ".FALSE. .TRUE." ; int LnudgeTCLM(tracer) ; LnudgeTCLM:long_name = "tracer climatology nudging activation switch" ; LnudgeTCLM:flag_values = 0, 1 ; LnudgeTCLM:flag_meanings = ".FALSE. .TRUE." ; int BioIter ; BioIter:long_name = "number of iterations to achieve convergence" ; double AttSW ; AttSW:long_name = "light attenuation by seawater" ; AttSW:units = "meter-1" ; double AttChl ; AttChl:long_name = "light attenuation by chlorophyll" ; AttChl:units = "meter-2 milligram_Chl-1" ; double PARfrac ; PARfrac:long_name = "photosynthetically available radiation fraction" ; double Vp0 ; Vp0:long_name = "Eppley temperature-limited growth parameter" ; double I_thNH4 ; I_thNH4:long_name = "radiation threshold for nitrification" ; I_thNH4:units = "watt meter-2" ; double D_p5NH4 ; D_p5NH4:long_name = "half-saturation radiation for nitrification" ; D_p5NH4:units = "watt meter-2" ; double NitriR ; NitriR:long_name = "nitrification rate" ; NitriR:units = "day-1" ; double K_NO3 ; K_NO3:long_name = "inverse half-saturation for phytoplankton NO3 uptake" ; K_NO3:units = "meter3 millimole_N-1" ; double K_NH4 ; K_NH4:long_name = "inverse half-saturation for phytoplankton NH4 uptake" ; K_NH4:units = "meter3 millimole_N-1" ; double K_Phy ; K_Phy:long_name = "zooplankton half-saturation constant for ingestion" ; K_Phy:units = "day-1" ; double Chl2C_m ; Chl2C_m:long_name = "maximum chlorophyll to carbon ratio" ; Chl2C_m:units = "milligram_chl milligram_carbon-1" ; double ChlMin ; ChlMin:long_name = "minimum chlorophyll threshold" ; ChlMin:units = "milligram_chl meter-3" ; double PhyCN ; PhyCN:long_name = "phytoplankton Carbon:Nitrogen ratio" ; PhyCN:units = "mole_C mole_N-1" ; double PhyIP ; PhyIP:long_name = "phytoplankton, NH4 inhibition parameter" ; PhyIP:units = "millimole_N-1" ; double PhyIS ; PhyIS:long_name = "phytoplankton, initial slope of P-I curve" ; PhyIS:units = "milligram_C milligram_Chl-1 watt-1 meter2 day-1" ; double PhyMin ; PhyMin:long_name = "minimum phytoplankton threshold" ; PhyMin:units = "millimole_N meter-3" ; double PhyMR ; PhyMR:long_name = "phytoplankton mortality rate" ; PhyMR:units = "day-1" ; double ZooAE_N ; ZooAE_N:long_name = "zooplankton mitrogen assimilation efficiency" ; double ZooBM ; ZooBM:long_name = "rate for zooplankton basal metabolism" ; ZooBM:units = "day-1" ; double ZooCN ; ZooCN:long_name = "zooplankton Carbon:Nitrogen ratio" ; ZooCN:units = "mole_C mole_N-1" ; double ZooER ; ZooER:long_name = "zooplankton specific excretion rate" ; ZooER:units = "day-1" ; double ZooGR ; ZooGR:long_name = "zooplankton maximum growth rate" ; ZooGR:units = "day-1" ; double ZooMin ; ZooMin:long_name = "minimum zooplankton threshold" ; ZooMin:units = "millimole_N meter-3" ; double ZooMR ; ZooMR:long_name = "zooplankton mortality rate" ; ZooMR:units = "day-1" ; double LDeRRN ; LDeRRN:long_name = "rate of large detritus nitrogen re-mineralization" ; LDeRRN:units = "day-1" ; double LDeRRC ; LDeRRC:long_name = "rate of large detritus carbon re-mineralization" ; LDeRRC:units = "day-1" ; double CoagR ; CoagR:long_name = "coagulation rate" ; CoagR:units = "day-1" ; double SDeRRN ; SDeRRN:long_name = "remineralization rate for small detritus nitrogen" ; SDeRRN:units = "day-1" ; double SDeRRC ; SDeRRC:long_name = "remineralization rate for small detritus carbon" ; SDeRRC:units = "day-1" ; double wPhy ; wPhy:long_name = "vertical sinking velocity for phytoplankton" ; wPhy:units = "meter day-1" ; double wLDet ; wLDet:long_name = "vertical sinking velocity for large detritus" ; wLDet:units = "meter day-1" ; double wSDet ; wSDet:long_name = "vertical sinking velocity for small detritus" ; wSDet:units = "meter day-1" ; double pCO2air ; pCO2air:long_name = "partial pressure of CO2 in the air" ; pCO2air:units = "parts per million by volume" ; int spherical ; spherical:long_name = "grid type logical switch" ; spherical:flag_values = 0, 1 ; spherical:flag_meanings = "Cartesian spherical" ; double xl ; xl:long_name = "domain length in the XI-direction" ; xl:units = "meter" ; double el ; el:long_name = "domain length in the ETA-direction" ; el:units = "meter" ; int Vtransform ; Vtransform:long_name = "vertical terrain-following transformation equation" ; int Vstretching ; Vstretching:long_name = "vertical terrain-following stretching function" ; double theta_s ; theta_s:long_name = "S-coordinate surface control parameter" ; double theta_b ; theta_b:long_name = "S-coordinate bottom control parameter" ; double Tcline ; Tcline:long_name = "S-coordinate surface/bottom layer width" ; Tcline:units = "meter" ; double hc ; hc:long_name = "S-coordinate parameter, critical depth" ; hc:units = "meter" ; double s_rho(s_rho) ; s_rho:long_name = "S-coordinate at RHO-points" ; s_rho:valid_min = -1. ; s_rho:valid_max = 0. ; s_rho:positive = "up" ; s_rho:standard_name = "ocean_s_coordinate_g1" ; s_rho:formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc" ; s_rho:field = "s_rho, scalar" ; double s_w(s_w) ; s_w:long_name = "S-coordinate at W-points" ; s_w:valid_min = -1. ; s_w:valid_max = 0. ; s_w:positive = "up" ; s_w:standard_name = "ocean_s_coordinate_g1" ; s_w:formula_terms = "s: s_w C: Cs_w eta: zeta depth: h depth_c: hc" ; s_w:field = "s_w, scalar" ; double Cs_r(s_rho) ; Cs_r:long_name = "S-coordinate stretching curves at RHO-points" ; Cs_r:valid_min = -1. ; Cs_r:valid_max = 0. ; Cs_r:field = "Cs_r, scalar" ; double Cs_w(s_w) ; Cs_w:long_name = "S-coordinate stretching curves at W-points" ; Cs_w:valid_min = -1. ; Cs_w:valid_max = 0. ; Cs_w:field = "Cs_w, scalar" ; double h(eta_rho, xi_rho) ; h:long_name = "bathymetry at RHO-points" ; h:units = "meter" ; h:coordinates = "lon_rho lat_rho" ; h:field = "bath, scalar" ; double f(eta_rho, xi_rho) ; f:long_name = "Coriolis parameter at RHO-points" ; f:units = "second-1" ; f:coordinates = "lon_rho lat_rho" ; f:field = "coriolis, scalar" ; double pm(eta_rho, xi_rho) ; pm:long_name = "curvilinear coordinate metric in XI" ; pm:units = "meter-1" ; pm:coordinates = "lon_rho lat_rho" ; pm:field = "pm, scalar" ; double pn(eta_rho, xi_rho) ; pn:long_name = "curvilinear coordinate metric in ETA" ; pn:units = "meter-1" ; pn:coordinates = "lon_rho lat_rho" ; pn:field = "pn, scalar" ; double lon_rho(eta_rho, xi_rho) ; lon_rho:long_name = "longitude of RHO-points" ; lon_rho:units = "degree_east" ; lon_rho:standard_name = "longitude" ; lon_rho:field = "lon_rho, scalar" ; double lat_rho(eta_rho, xi_rho) ; lat_rho:long_name = "latitude of RHO-points" ; lat_rho:units = "degree_north" ; lat_rho:standard_name = "latitude" ; lat_rho:field = "lat_rho, scalar" ; double lon_u(eta_u, xi_u) ; lon_u:long_name = "longitude of U-points" ; lon_u:units = "degree_east" ; lon_u:standard_name = "longitude" ; lon_u:field = "lon_u, scalar" ; double lat_u(eta_u, xi_u) ; lat_u:long_name = "latitude of U-points" ; lat_u:units = "degree_north" ; lat_u:standard_name = "latitude" ; lat_u:field = "lat_u, scalar" ; double lon_v(eta_v, xi_v) ; lon_v:long_name = "longitude of V-points" ; lon_v:units = "degree_east" ; lon_v:standard_name = "longitude" ; lon_v:field = "lon_v, scalar" ; double lat_v(eta_v, xi_v) ; lat_v:long_name = "latitude of V-points" ; lat_v:units = "degree_north" ; lat_v:standard_name = "latitude" ; lat_v:field = "lat_v, scalar" ; double lon_psi(eta_psi, xi_psi) ; lon_psi:long_name = "longitude of PSI-points" ; lon_psi:units = "degree_east" ; lon_psi:standard_name = "longitude" ; lon_psi:field = "lon_psi, scalar" ; double lat_psi(eta_psi, xi_psi) ; lat_psi:long_name = "latitude of PSI-points" ; lat_psi:units = "degree_north" ; lat_psi:standard_name = "latitude" ; lat_psi:field = "lat_psi, scalar" ; double angle(eta_rho, xi_rho) ; angle:long_name = "angle between XI-axis and EAST" ; angle:units = "radians" ; angle:coordinates = "lon_rho lat_rho" ; angle:field = "angle, scalar" ; double mask_rho(eta_rho, xi_rho) ; mask_rho:long_name = "mask on RHO-points" ; mask_rho:flag_values = 0., 1. ; mask_rho:flag_meanings = "land water" ; mask_rho:coordinates = "lon_rho lat_rho" ; double mask_u(eta_u, xi_u) ; mask_u:long_name = "mask on U-points" ; mask_u:flag_values = 0., 1. ; mask_u:flag_meanings = "land water" ; mask_u:coordinates = "lon_u lat_u" ; double mask_v(eta_v, xi_v) ; mask_v:long_name = "mask on V-points" ; mask_v:flag_values = 0., 1. ; mask_v:flag_meanings = "land water" ; mask_v:coordinates = "lon_v lat_v" ; double mask_psi(eta_psi, xi_psi) ; mask_psi:long_name = "mask on psi-points" ; mask_psi:flag_values = 0., 1. ; mask_psi:flag_meanings = "land water" ; mask_psi:coordinates = "lon_psi lat_psi" ; double ocean_time(ocean_time) ; ocean_time:long_name = "time since initialization" ; ocean_time:units = "seconds since 1858-11-17 00:00:00" ; ocean_time:calendar = "gregorian" ; ocean_time:field = "time, scalar, series" ; float zeta(ocean_time, eta_rho, xi_rho) ; zeta:long_name = "free-surface" ; zeta:units = "meter" ; zeta:time = "ocean_time" ; zeta:coordinates = "lon_rho lat_rho ocean_time" ; zeta:field = "free-surface, scalar, series" ; zeta:_FillValue = 1.e+37f ; float ubar(ocean_time, eta_u, xi_u) ; ubar:long_name = "vertically integrated u-momentum component" ; ubar:units = "meter second-1" ; ubar:time = "ocean_time" ; ubar:coordinates = "lon_u lat_u ocean_time" ; ubar:field = "ubar-velocity, scalar, series" ; ubar:_FillValue = 1.e+37f ; float vbar(ocean_time, eta_v, xi_v) ; vbar:long_name = "vertically integrated v-momentum component" ; vbar:units = "meter second-1" ; vbar:time = "ocean_time" ; vbar:coordinates = "lon_v lat_v ocean_time" ; vbar:field = "vbar-velocity, scalar, series" ; vbar:_FillValue = 1.e+37f ; float u(ocean_time, s_rho, eta_u, xi_u) ; u:long_name = "u-momentum component" ; u:units = "meter second-1" ; u:time = "ocean_time" ; u:coordinates = "lon_u lat_u s_rho ocean_time" ; u:field = "u-velocity, scalar, series" ; u:_FillValue = 1.e+37f ; float v(ocean_time, s_rho, eta_v, xi_v) ; v:long_name = "v-momentum component" ; v:units = "meter second-1" ; v:time = "ocean_time" ; v:coordinates = "lon_v lat_v s_rho ocean_time" ; v:field = "v-velocity, scalar, series" ; v:_FillValue = 1.e+37f ; float w(ocean_time, s_w, eta_rho, xi_rho) ; w:long_name = "vertical momentum component" ; w:units = "meter second-1" ; w:time = "ocean_time" ; w:coordinates = "lon_rho lat_rho s_w ocean_time" ; w:field = "w-velocity, scalar, series" ; w:_FillValue = 1.e+37f ; float temp(ocean_time, s_rho, eta_rho, xi_rho) ; temp:long_name = "potential temperature" ; temp:units = "Celsius" ; temp:time = "ocean_time" ; temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ; temp:field = "temperature, scalar, series" ; temp:_FillValue = 1.e+37f ; float salt(ocean_time, s_rho, eta_rho, xi_rho) ; salt:long_name = "salinity" ; salt:time = "ocean_time" ; salt:coordinates = "lon_rho lat_rho s_rho ocean_time" ; salt:field = "salinity, scalar, series" ; salt:_FillValue = 1.e+37f ; float NO3(ocean_time, s_rho, eta_rho, xi_rho) ; NO3:long_name = "nitrate concentration" ; NO3:units = "millimole_N03 meter-3" ; NO3:time = "ocean_time" ; NO3:coordinates = "lon_rho lat_rho s_rho ocean_time" ; NO3:field = "NO3, scalar, series" ; NO3:_FillValue = 1.e+37f ; float NH4(ocean_time, s_rho, eta_rho, xi_rho) ; NH4:long_name = "ammonium concentration" ; NH4:units = "millimole_NH4 meter-3" ; NH4:time = "ocean_time" ; NH4:coordinates = "lon_rho lat_rho s_rho ocean_time" ; NH4:field = "NH4, scalar, series" ; NH4:_FillValue = 1.e+37f ; float chlorophyll(ocean_time, s_rho, eta_rho, xi_rho) ; chlorophyll:long_name = "chlorophyll concentration" ; chlorophyll:units = "milligrams_chlorophyll meter-3" ; chlorophyll:time = "ocean_time" ; chlorophyll:coordinates = "lon_rho lat_rho s_rho ocean_time" ; chlorophyll:field = "chlorophyll, scalar, series" ; chlorophyll:_FillValue = 1.e+37f ; float phytoplankton(ocean_time, s_rho, eta_rho, xi_rho) ; phytoplankton:long_name = "phytoplankton concentration" ; phytoplankton:units = "millimole_nitrogen meter-3" ; phytoplankton:time = "ocean_time" ; phytoplankton:coordinates = "lon_rho lat_rho s_rho ocean_time" ; phytoplankton:field = "phytoplankton, scalar, series" ; phytoplankton:_FillValue = 1.e+37f ; float zooplankton(ocean_time, s_rho, eta_rho, xi_rho) ; zooplankton:long_name = "zooplankton concentration" ; zooplankton:units = "millimole_nitrogen meter-3" ; zooplankton:time = "ocean_time" ; zooplankton:coordinates = "lon_rho lat_rho s_rho ocean_time" ; zooplankton:field = "zooplankton, scalar, series" ; zooplankton:_FillValue = 1.e+37f ; // global attributes: :file = "/gpfs_share/omg/autosabgom/out/his_20170405_0002.nc" ; :format = "netCDF-3 64bit offset file" ; :Conventions = "CF-1.4" ; :type = "ROMS/TOMS history file" ; :title = "South-Atlantic Bight and Gulf of Mexico Application" ; :var_info = "/gpfs_share/jbzambon/nf_centos7/roms_sabgom_nf/ROMS/External/varinfo.dat" ; :rst_file = "/gpfs_share/omg/autosabgom/out/rst_20170405.nc" ; :his_base = "/gpfs_share/omg/autosabgom/out/his_20170405" ; :dia_file = "/gpfs_share/omg/autosabgom/out/dia_20170405.nc" ; :sta_file = "/gpfs_share/omg/autosabgom/out/sta_20170405.nc" ; :grd_file = "/gpfs_share/omg/omg/autosabgom/in/sabgom_grd.nc.Etopo2.LP.r1_5.filled" ; :ini_file = "/gpfs_share/omg/omg/autosabgom/in/ncoda_ini_20170405.nc" ; :frc_file_01 = "/gpfs_share/omg/omg/autosabgom/in/nomads_forc_20170405.nc" ; :frc_file_02 = "/gpfs_share/omg/omg/autosabgom/in/SABGOM.OTIS.Ref18581117.8Cons" ; :bry_file = "/gpfs_share/omg/omg/autosabgom/in/ncoda_bry_20170405.nc" ; :clm_file = "/gpfs_share/omg/omg/autosabgom/in/ncoda_clm_20170405.nc" ; :nud_file = "/gpfs_share/omg/omg/autosabgom/in/sabgom_nudgcoef_from_ananug.nc" ; :script_file = "" ; :bpar_file = "/home/omg/autosabgom/bioFasham_038_Katja.in.U3C4" ; :spos_file = "/home/omg/autosabgom/stations.in" ; :NLM_LBC = "\n", "EDGE: WEST SOUTH EAST NORTH \n", "zeta: Clo Cha Cha Clo \n", "ubar: Clo Fla Fla Clo \n", "vbar: Clo Fla Fla Clo \n", "u: Clo RadNud RadNud Clo \n", "v: Clo RadNud RadNud Clo \n", "temp: Clo RadNud RadNud Clo \n", "salt: Clo RadNud RadNud Clo \n", "NO3: Clo RadNud RadNud Clo \n", "NH4: Clo RadNud RadNud Clo \n", "chlorophyll: Clo RadNud RadNud Clo \n", "phytoplankton: Clo RadNud RadNud Clo \n", "zooplankton: Clo RadNud RadNud Clo \n", "LdetritusN: Clo RadNud RadNud Clo \n", "SdetritusN: Clo RadNud RadNud Clo \n", "LdetritusC: Clo RadNud RadNud Clo \n", "SdetritusC: Clo RadNud RadNud Clo \n", "TIC: Clo RadNud RadNud Clo \n", "alkalinity: Clo RadNud RadNud Clo \n", "oxygen: Clo RadNud RadNud Clo \n", "tke: Clo Gra Gra Clo" ; :svn_url = "https://www.myroms.org/svn/src/trunk" ; :svn_rev = "Unversioned directory" ; :code_dir = "/gpfs_share/jbzambon/nf_centos7/roms_sabgom_nf" ; :header_dir = "/gpfs_share/jbzambon/nf_centos7/roms_sabgom_nf/ROMS/Include" ; :header_file = "sabgom_bio.h" ; :os = "Linux" ; :cpu = "x86_64" ; :compiler_system = "ifort" ; :compiler_command = "/usr/local/apps/mpich3/centos7/intelmpi2016/mpif90" ; :compiler_flags = "-heap-arrays -fp-model precise -ip -O3 -free -free" ; :tiling = "007x004" ; :history = "ROMS/TOMS, Version 3.7, Wednesday - April 5, 2017 - 2:47:56 AM" ; :ana_file = "ROMS/Functionals/ana_btflux.h, ROMS/Functionals/ana_stflux.h" ; :bio_file = "ROMS/Nonlinear/Biology/fennel.h" ; :CPP_options = "SABGOM_BIO, ADD_FSOBC, ADD_M2OBC, ANA_BPFLUX, ANA_BSFLUX, ANA_BTFLUX, ANA_SPFLUX, ASSUMED_SHAPE, BIO_FENNEL, BIO_SEDIMENT, BULK_FLUXES, CARBON, CURVGRID, DENITRIFICATION, DIAGNOSTICS_BIO, DJ_GRADPS, DOUBLE_PRECISION, EMINUSP, KANTHA_CLAYSON, MASKING, MIX_GEO_TS, MIX_S_UV, MPI, MY25_MIXING, NONLINEAR, NONLIN_EOS, N2S2_HORAVG, !OCMIP_OXYGEN_SC, OXYGEN, POWER_LAW, PROFILE, K_GSCHEME, RADIATION_2D, RAMP_TIDES, !RST_SINGLE, SALINITY, SOLAR_SOURCE, SOLVE3D, SSH_TIDES, STATIONS, !TALK_NONCONSERV, TS_U3HADVECTION, TS_C4VADVECTION, TS_DIF2, UV_ADV, UV_COR, UV_U3HADVECTION, UV_C4VADVECTION, UV_QDRAG, UV_TIDES, UV_VIS2, VAR_RHO_2D" ; } ************************************************

On Apr 5, 2017, at 9:58 AM, Kyle Wilcox ***@***.***> wrote: The additional time dimensions have dropped off of the DAP aggregation now and its back to only time: http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom/SABGOM_Forecast_Model_Run_Collection_best.ncd.html <http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom/SABGOM_Forecast_Model_Run_Collection_best.ncd.html>. Does newer data not have any of the variables that were dimensioned by those? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMOXrslKo0HQRA7uTH6O6gpWybRbZylLks5rs530gaJpZM4Mu6OO>.

[rsignell-usgs]

Hmm, the start/stop times for SABGOM are currently:
2017-Feb-27 15:00
2017-Apr-08 00:00

Is that correct?

[rsignell-usgs]

import netCDF4

def start_stop(url,tvar):
    nc = netCDF4.Dataset(url)
    ncv = nc.variables
    time_var = ncv[tvar]
    first = netCDF4.num2date(time_var[0],time_var.units)
    last = netCDF4.num2date(time_var[-1],time_var.units)

    print first.strftime('%Y-%b-%d %H:%M')
    print last.strftime('%Y-%b-%d %H:%M')

url='http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom/SABGOM_Forecast_Model_Run_Collection_best.ncd'
tvar='time'
start_stop(url,tvar)

yields

2017-Feb-27 15:00
2017-Apr-08 00:00

[jbzambon]

Ah, yes, I was looking at the archive, not the past month. oceanus, not omgsrv1. But yes, we've had a few iterations since the dataset begins in 2010. The most recent was a few months back when I needed to recompile ROMS for new hardware as our original queue aged out at 9 years.

…

-Joe

On Apr 5, 2017, at 10:05 AM, Rich Signell ***@***.***> wrote: import netCDF4 def start_stop(url,tvar): nc = netCDF4.Dataset(url) ncv = nc.variables time_var = ncv[tvar] first = netCDF4.num2date(time_var[0],time_var.units) last = netCDF4.num2date(time_var[-1],time_var.units) print first.strftime('%Y-%b-%d %H:%M') print last.strftime('%Y-%b-%d %H:%M') url='http://omgsrv1.meas.ncsu.edu:8080/thredds/dodsC/fmrc/sabgom/SABGOM_Forecast_Model_Run_Collection_best.ncd' tvar='time' start_stop(url,tvar) yeilds 2017-Feb-27 15:00 2017-Apr-08 00:00 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMOXrhPrMDbdTHiC_uqXG9wmw31B4FCuks5rs5-VgaJpZM4Mu6OO>.