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Jordan S Read
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Merge pull request #225 from jread-usgs/master
update for hanging line parser error
2 parents 4b47372 + ef75ffb commit bca248c

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‎DESCRIPTION

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Package: glmtools
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Type: Package
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Title: glmtools
4-
Version: 0.14.4
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Version: 0.14.5
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Date: 2017-01-11
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Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
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email = "[email protected]"),

‎R/nml_helpers.R

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@@ -17,6 +17,10 @@ buildVal <- function(textLine, lineNum, blckName){
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# can be: string, number, comma-sep-numbers, or boolean
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# special case for date:
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if (is.na(parVl)){
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stop('Empty values after "', textLine, '" on line ', lineNum,
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'. \nPerhaps the values are on the next line?', call. = FALSE)
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}
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if (nchar(parVl>17) & substr(parVl,14,14)==':' & substr(parVl,17,17)==':'){
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parVl<-paste(c(substr(parVl,1,11),' ',substr(parVl,12,nchar(parVl))),collapse='')
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}

‎inst/extdata/hanging_line.nml

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!-------------------------------------------------------------------------------
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! general model setup
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!-------------------------------------------------------------------------------
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!
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! sim_name [string] title of simulation
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! max_layers [integer] maximum number of layers
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! min_layer_vol [real] minimum layer volume (m3 * 1000)
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! min_layer_thick [real] minimum layer thickness (m)
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! max_layer_thick [real] maximum layer thickness (m)
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! Kw [real] background light attenuation (m**-1)
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! coef_mix_conv [real] mixing efficiency - convective overturn
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! coef_wind_stir [real] mixing efficiency - wind stirring
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! coef_mix_turb [real] mixing efficiency - unsteady turbulence effects
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! coef_mix_shear [real] mixing efficiency - shear production !sensitive to hypolimnetic temperature
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! coef_mix_KH [real] mixing efficiency - hypolimnetic Kelvin-Helmholtz turbulent billows
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! coef_mix_hyp [real] mixing efficiency - hypolimnetic turbulence
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! deep_mixing [bool] flag to disable deep-mixing
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!
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!-------------------------------------------------------------------------------
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&glm_setup
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sim_name = 'GLM Simulation'
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max_layers = 500
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min_layer_vol = 0.025
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min_layer_thick = 0.05
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!min_layer_thick = 0.350
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max_layer_thick = 0.500
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!max_layer_thick = 0.900
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!-- Light Parameters
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Kw = 0.85
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!-- Mixing Parameters
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coef_mix_conv = 0.125 ! 0.05,0.2 , 0.35 , 0.12
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coef_wind_stir = 0.23 ! 0.1,0.3, 0.3, 0.1
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coef_mix_shear = 0.2 ! 0.018,0.4, 0.2, 0.13
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coef_mix_turb = 0.51 ! 0.51, 0.51, 0.51, 0.51
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coef_mix_KH = 0.33 !0.015, 0.4, 0.18, 0.33
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coef_mix_hyp = 0.5 !0.05, 0.6, 0.25, 0.8
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! non_avg = .true.
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! deep_mixing = .true.
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/
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!-------------------------------------------------------------------------------
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! wq setup
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! if this block is read, water quality functionality will be enabled
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!-------------------------------------------------------------------------------
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! wq_lib [string]
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! Select which WQ library to use;
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! valid options are 'aed2' or 'fabm' [default is 'aed2']
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! ode_method [integer]
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! ODE numerical scheme for source and sink dynamics
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! 1: first-order explicit (not positive)
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! 2: second-order explicit Runge-Kutta (not positive)
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! 3: fourth-order explicit Runge-Kutta (not positive)
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! 4: Patankar (first-order, not conservative)
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! 5: Patankar-RK (second-order, not conservative)
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! 6: Patankar-RK (does not work, not conservative)
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! 7: Modified Patankar (1st-order, conservat., posit.)
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! 8: Modified Patankar-RK (2nd-order, conservat., posit.)
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! 9: Modified Patankar-RK (does not work, conservat.,
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! posit.)
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! 10: Extended Modified Patankar (1st-order, conservat.,
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! posit.)
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! 11: Extended Modified Patankar-RK (2nd-order, conservat.,
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! posit.)
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! This variable is used only if bio_calc = True
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! split_factor [integer, minimum = 1]
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! number of biogeochemical time steps per physical time step
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! bioshade_feedback [bool]
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! feedback of bio-turbidity to temperature equation
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! repair_state [bool]
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! FABM option to repeair state variables that have -ve's
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! wq_nml_file [string]
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! name of .nml file to be passed to WQ library;
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! the default is {wq_lib}.nml (eg aed2.nml)
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! mobility_off [bool]
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! flag to turn off settling/rising
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! multi_ben [bool]
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! GLM specific option for FABM to do benthic fluxes only
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! in bottom layer, or on flanks of all layers (.true.)
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!-------------------------------------------------------------------------------
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&wq_setup
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wq_lib = 'aed2'
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wq_nml_file = 'aed2.nml'
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ode_method = 1
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split_factor = 1
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!bioshade_feedback = .true.
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bioshade_feedback = .false.
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repair_state = .true.
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! mobility_off = .false.
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multi_ben = .true.
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/
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!-------------------------------------------------------------------------------
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! lake details
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!-------------------------------------------------------------------------------
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!
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! name [string]
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! name of the lake
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! latitude [float, minimum = -90, maximum = 90, unit = deg North]
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! latitude
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! longitude [float, minimum = -360, maximum = 360, unit = deg East]
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! longitude
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! base_elev [float]
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! base elevation (m)
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! crest_elev [float]
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! crest elevation (m)
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! bsn_len [float]
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! basin length at crest (m)
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! bsn_wid [float]
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! basin width at crest (m)
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! bsn_vals [integer]
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! number of depth points on height-area relationship
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! H [float]
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! elevations (m) (comma separated list, len=bsn_vals)
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! A [float]
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! area (m2) (comma separated list, len=bsn_vals)
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!
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!-------------------------------------------------------------------------------
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&morphometry
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lake_name = 'Falling Creek'
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latitude = 37.307681
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longitude = -79.837068
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bsn_len = 711.699
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bsn_wid = 226.030
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bsn_vals = 31
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! H(m) A(m2) V(m3)
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H = 497.683,497.983,498.283,498.683,498.983,499.283,499.583,499.883,500.183,500.483,500.783,501.083,501.383,501.683,501.983,502.283,502.583,502.883,503.183,503.483,503.783,504.083,504.383,504.683,505.083,505.383,505.683,505.983,506.283,506.583,506.983
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A = 0,61.408883,494.615572,1201.23579,2179.597283,3239.620513,4358.358439,5637.911458,6929.077352,8228.697419,9469.324081,10811.30792,12399.67051,14484.22802,16834.20941,19631.05422,22583.1399,25790.70893,28442.99667,31155.95008,36269.3312,42851.13714,51179.89109,59666.85885,68146.39437,76424.14457,85430.25429,95068.47603,103030.4489,111302.1604,119880.9164
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/
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!-------------------------------------------------------------------------------
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! duration of run
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!-------------------------------------------------------------------------------
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!
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! timefmt [integer]
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! method to specify start and duration of model run
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! 1: duration computed from number of time steps, MaxN (bogus start
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! date used) [no longer implemented!!]
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! 2: duration computed from given start and stop dates (number of time
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! steps MaxN computed)
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! 3: duration computed from number of time steps, MaxN (start date as
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! specified, stop date computed)
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! start [string, format = "yyyy-mm-dd hh:mm:ss"]
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! nominal start date
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! This variable is used only if timefmt != 1
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! stop [string, format = "yyyy-mm-dd hh:mm:ss"]
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! nominal stop date
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! This variable is used only if timefmt = 2
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! dt [float, minimum = 0.001, maximum = 86400, unit = s]
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! Time step for integration
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! numb_days [number of days to run the simulation ]
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! This variable is used only if timefmt != 2
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!
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!-------------------------------------------------------------------------------
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&time
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timefmt = 2
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start = '2015-03-31 11:00:00'
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stop = '2015-09-30 00:00:00'
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dt = 3600.0
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!num_days = 3288
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timezone = -5.0
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/
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!-------------------------------------------------------------------------------
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! format for output and filename(s)
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!-------------------------------------------------------------------------------
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!
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! out_dir [string]
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! path to output directory (set permissions)
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! out_fn [string]
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! name of output netcdf file
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! nsave [integer, minimum = 1, maximum = 86400]
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! save results every 'nsave' timesteps
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! csv_lake_fname [string]
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! name of lake.csv lake simulation daily summary information
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! csv_point_nlevs [integer]
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! number of depths at which to dump a csv time-series file
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! csv_point_at [real]
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! height from bottom for point csv file(s) (comma separated list)
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! csv_point_fname [string]
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! name of csv output file(s) (comma separated list)
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! csv_point_nvars [integer]
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! number of variables to output into csv
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! csv_point_vars [string]
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! list of names of variables to output, - order IS important
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! csv_outlet_allinone [bool]
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! put all outflow data into the same csv file
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! csv_outlet_fname [string]
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! name of csv output file(s) (comma separated list)
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! csv_outlet_nvars [integer]
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! number of variables to output into outlet csv
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! csv_outlet_vars [string]
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! list of names of variables to output
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! csv_ovrflw_fname [string]
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! name of csv file to record amount and quality of overflow
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!
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!-------------------------------------------------------------------------------! simulation number 1
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&output
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out_dir = '.'
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out_fn = 'output'
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nsave = 24
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csv_point_nlevs = 2
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csv_point_fname = 'WQ_'
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csv_point_at = 20,22
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csv_point_nvars = 6
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csv_lake_fname = 'Physics'
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csv_point_vars = 'temp','OXY_oxy','PHY_CYANOPCH1','PHY_CYANONPCH2','PHY_CHLOROPCH3','PHY_DIATOMPCH4'
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/
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!-------------------------------------------------------------------------------
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! initial condition profiles
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!-------------------------------------------------------------------------------
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!
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! lake_depth [float] initial lake depth (m)
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! num_depths [integer] number of depths provided for initial profiles
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! the_depths [float] the depths of the initial profile points (m)
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! the_temps [float] the temperature of the initial profile points (C)
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! the_sals [float] the salinity of the initial profile points (psu)
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! num_wq_vars [integer] number of non GLM (ie FABM) vars to be initialised
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! wq_names [string] names of non GLM (ie FABM) vars to be initialised
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! wq_init_vals [float] array of FABM vars (rows = vars; cols = depths)
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!
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!-------------------------------------------------------------------------------
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&init_profiles
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num_depths = 30
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lake_depth = 9.3
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the_depths = 0.0, 0.80, 1.11, 1.41, 1.71, 2.02, 2.32, 2.62, 2.93, 3.23, 3.53, 3.84, 4.14, 4.44, 4.75, 5.05, 5.36, 5.66, 5.96, 6.27, 6.57, 6.87, 7.18, 7.48, 7.78, 8.09, 8.39, 8.69, 9.00, 9.30,
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the_temps = 5.80, 5.82, 5.89, 5.95, 6.02, 6.09, 6.18, 6.25, 6.36, 6.45, 6.59, 6.73, 6.83, 6.91, 7.00, 7.08, 7.14, 7.23, 7.32, 7.42, 7.55, 7.69, 7.81, 8.01, 8.38, 8.66, 8.88, 8.93, 8.97, 9.12,
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the_sals = 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50
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num_wq_vars = 7
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wq_names =
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'OGM_doc',
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'OXY_oxy',
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'CAR_dic',
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'NIT_amm',
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'NIT_nit',
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'PHS_frp',
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'CAR_ch4'
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wq_init_vals = 0.09, 0.09, 0.09, 0.09, 0.09, 0.09, 0.09, 0.09, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.09, 0.09, 0.09, 0.09, 0.09, 0.09, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08,
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300.62, 300.41, 300.19, 300.98, 300.76, 300.55, 300.33, 300.12, 300.90, 300.69, 300.47, 300.25, 300.04, 300.82, 300.61, 300.39, 300.18, 300.96, 300.75, 300.53, 300.31, 300.10, 250.88, 250.67, 250.45, 250.24, 250.02, 250.81, 250.59, 250.38,
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0.11, 0.11, 0.11, 0.11, 0.11, 0.13, 0.13, 0.13, 0.13, 0.13, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.12, 0.13, 0.13, 0.13,
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0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.22, 0.25, 0.25, 0.25, 0.25, 0.25, 0.22, 0.22, 0.22, 0.22, 0.23, 0.23, 0.23, 0.23, 0.23, 0.26, 0.26, 0.26, 0.37, 0.37,
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0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.19, 0.17, 0.17, 0.17, 0.17, 0.17, 0.12, 0.12, 0.12, 0.12, 0.15, 0.15, 0.15, 0.15, 0.15, 0.20, 0.20, 0.20, 0.21, 0.21,
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0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.63, 0.63, 0.63, 0.63, 0.63, 0.63, 0.53, 0.53, 0.53, 0.53, 0.53, 0.47, 0.47, 0.47, 0.47, 0.47, 0.53, 0.53, 0.51, 0.51, 0.51, 0.51,
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0.58, 0.58, 0.59, 0.59, 0.60, 0.60, 0.61, 0.61, 0.62, 0.62, 0.62, 0.63, 0.63, 0.64, 0.64, 0.65, 0.65, 0.66, 0.66, 0.67, 0.67, 0.67, 0.68, 0.68, 0.69, 0.69, 0.70, 0.70, 0.71, 0.71
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/
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!-------------------------------------------------------------------------------
246+
! meteorology
247+
!-------------------------------------------------------------------------------
248+
!
249+
! met_sw [bool] switch to include surface meteorological forcing
250+
! lw_type [string] type of longwave data supplied (LW_IN/LW_CC/LW_NET)
251+
! rain_sw [bool] include rainfall nutrient composition
252+
! snow_sw [bool] include snowfall (m/d)
253+
! atm_stab [bool] account for non-neutral atmospheric stability
254+
! catchrain [bool] flag that enables runoff from exposed banks of lake area
255+
! rad_mode [integer] short and long wave radation model configuration (see manual)
256+
! albedo_mode [integer] shortwave albedo calculation method
257+
! cloud_mode [integer] atmospheric emmisivity calculation method
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!
259+
! meteo_fl [string] name of file with meteorology input data
260+
! wind_factor [float] wind multiplication factor (-)
261+
! wind_factor [float] wind multiplication factor (-)
262+
! rain_factor [float] wind multiplication factor (-)
263+
! sw_factor [float] wind multiplication factor (-)
264+
! lw_factor [float] wind multiplication factor (-)
265+
! at_factor [float] wind multiplication factor (-)
266+
! rh_factor [float] wind multiplication factor (-)
267+
!
268+
! ce [float] bulk aerodynamic coefficient for latent heat transfer
269+
! ch [float] bulk aerodynamic coefficient for sensible heat transfer
270+
! cd [float] bulk aerodynamic coefficient for transfer of momentum
271+
! rain_threshold [float] rainfall amount (m) required before runoff from exposed banks
272+
! runoff_coef [float] conversion of rainfall to runoff in exposed lake banks
273+
!
274+
!-------------------------------------------------------------------------------
275+
&meteorology
276+
met_sw = .true.
277+
lw_type = 'LW_IN'
278+
rain_sw = .false.
279+
snow_sw = .false.
280+
atm_stab = .false.
281+
catchrain = .false.
282+
rad_mode = 1
283+
albedo_mode = 1
284+
cloud_mode = 4
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!-- BC file details
286+
meteo_fl = 'glm_met_2015_FCR_adjusted_tillDec.csv'
287+
!meteo_fl = 'glm_met_2015_FCR_adjusted_wind.csv'
288+
subdaily = .true.
289+
wind_factor = 1.0
290+
sw_factor = 1.0
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lw_factor = 1.0
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at_factor = 1.0
293+
rh_factor = 1.0
294+
rain_factor = 1.0
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cd = 0.001
296+
ce = 0.0013
297+
ch = 0.0013
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rain_threshold = 0.01
299+
runoff_coef = 0.3
300+
time_fmt = 'YYYY-MM-DD hh:mm:ss'
301+
/
302+
!-------------------------------------------------------------------------------
303+
! inflows
304+
!-------------------------------------------------------------------------------
305+
!
306+
! num_inflows [integer] number of inflowing streams (0+)
307+
! names_of_strms [string] names of streams (comma separated list)
308+
! strm_hf_angle [float] stream half angle (degrees)
309+
! strmbd_slope [float] streambed slope (degrees)
310+
! strmbd_drag [float] streambed drag coefficient (-)
311+
! inflow_factor [float] inflow flow rate multiplier (-)
312+
! inflow_fl [string] inflow data filename(s) (comma separated list)
313+
! inflow_varnum [integer] number of columns (excluding date) to be read
314+
! inflow_vars [string] variable names of inflow file columns
315+
! This should be a comma separated list, and must
316+
! include FLOW, SALT & TEMP (for GLM), and
317+
! optionally can include FABM var names.
318+
! coef_inf_entrain [real] entrainment coefficient for inflows
319+
!
320+
!-------------------------------------------------------------------------------
321+
&inflow
322+
num_inflows = 2
323+
names_of_strms = 'river1','SSS'
324+
subm_flag = .false.,.true.
325+
strm_hf_angle = 100.0,35.0 !Degree of channelization
326+
strmbd_slope = 0.573,0.1 !0.03-0.05 FCR inflow 0.03 SSS
327+
strmbd_drag = 0.0160,0.0160
328+
inflow_factor = 1,0.00314 !SSS 0.00314
329+
inflow_fl = 'FCR_GLM_iof_2015_modified_9Jan17.csv','FCR_GLM_SSSin_2015_004.csv'
330+
inflow_varnum = 10
331+
inflow_vars = 'FLOW',
332+
'TEMP',
333+
'SALT',
334+
'OGM_doc',
335+
'NIT_amm',
336+
'OXY_oxy',
337+
'NIT_nit',
338+
'PHS_frp',
339+
'TOT_tn',
340+
'TOT_tp'
341+
/
342+
!-------------------------------------------------------------------------------
343+
! outflows
344+
!-------------------------------------------------------------------------------
345+
!
346+
! num_outlet [integer] no. of outlets
347+
! flt_off_sw [bool] floating offtake switches
348+
! outl_elvs [float] outlet elevations (comma separated list)
349+
! bsn_len_outl [float] basin length at outlets (m)
350+
! bsn_wid_outl [float] basin width at outlets (m)
351+
! outflow_fl [string] outflow data file
352+
! outflow_factor [float] outflow flow rate multiplier (-)
353+
! seepage [bool] do seepage processing [default is off - ie no seepage]
354+
! seepage_rate [float] seepage rate of water (m/day) from bottom layer
355+
!
356+
!-------------------------------------------------------------------------------
357+
&outflow
358+
num_outlet = 4
359+
flt_off_sw = .false.,.false.,.false.,.false.
360+
outl_elvs = 506.9,498,506.9,506.9
361+
bsn_len_outl = 711.699,100,711.699,711.699 !711.699
362+
bsn_wid_outl = 226.030,10,226.030,226.030 !226.030
363+
outflow_fl = 'FCR_GLM_out1_2015.csv','FCR_GLM_SSSin_2015_004.csv','FCR_glm_out2_extra_2015.csv','FCR_glm_out_WTP_2015.csv'
364+
outflow_factor = 1,0.00314,1,1 ! inflow 0.3
365+
/

‎tests/testthat/test-get_outputNC.R

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Original file line numberDiff line numberDiff line change
@@ -17,6 +17,10 @@ test_that("get_wind", {
1717
expect_true(all(t_out == df[,1]))
1818
})
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20+
test_that("check hanging nml", {
21+
expect_error(read_nml(system.file(package='glmtools', 'extdata', 'hanging_line.nml')), "Empty values after")
22+
})
23+
2024
context("get_surface_height")
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test_that("get_surface_height", {

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