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Merge pull request #225 from jread-usgs/master
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update for hanging line parser error
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Jordan S Read authored Jan 11, 2017
2 parents 4b47372 + ef75ffb commit bca248c
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: glmtools
Type: Package
Title: glmtools
Version: 0.14.4
Version: 0.14.5
Date: 2017-01-11
Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
email = "jread@usgs.gov"),
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4 changes: 4 additions & 0 deletions R/nml_helpers.R
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Expand Up @@ -17,6 +17,10 @@ buildVal <- function(textLine, lineNum, blckName){
# can be: string, number, comma-sep-numbers, or boolean

# special case for date:
if (is.na(parVl)){
stop('Empty values after "', textLine, '" on line ', lineNum,
'. \nPerhaps the values are on the next line?', call. = FALSE)
}
if (nchar(parVl>17) & substr(parVl,14,14)==':' & substr(parVl,17,17)==':'){
parVl<-paste(c(substr(parVl,1,11),' ',substr(parVl,12,nchar(parVl))),collapse='')
}
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365 changes: 365 additions & 0 deletions inst/extdata/hanging_line.nml
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!-------------------------------------------------------------------------------
! general model setup
!-------------------------------------------------------------------------------
!
! sim_name [string] title of simulation
! max_layers [integer] maximum number of layers
! min_layer_vol [real] minimum layer volume (m3 * 1000)
! min_layer_thick [real] minimum layer thickness (m)
! max_layer_thick [real] maximum layer thickness (m)
! Kw [real] background light attenuation (m**-1)
! coef_mix_conv [real] mixing efficiency - convective overturn
! coef_wind_stir [real] mixing efficiency - wind stirring
! coef_mix_turb [real] mixing efficiency - unsteady turbulence effects
! coef_mix_shear [real] mixing efficiency - shear production !sensitive to hypolimnetic temperature
! coef_mix_KH [real] mixing efficiency - hypolimnetic Kelvin-Helmholtz turbulent billows
! coef_mix_hyp [real] mixing efficiency - hypolimnetic turbulence
! deep_mixing [bool] flag to disable deep-mixing
!
!-------------------------------------------------------------------------------
&glm_setup
sim_name = 'GLM Simulation'
max_layers = 500
min_layer_vol = 0.025
min_layer_thick = 0.05
!min_layer_thick = 0.350
max_layer_thick = 0.500
!max_layer_thick = 0.900
!-- Light Parameters
Kw = 0.85
!-- Mixing Parameters
coef_mix_conv = 0.125 ! 0.05,0.2 , 0.35 , 0.12
coef_wind_stir = 0.23 ! 0.1,0.3, 0.3, 0.1
coef_mix_shear = 0.2 ! 0.018,0.4, 0.2, 0.13
coef_mix_turb = 0.51 ! 0.51, 0.51, 0.51, 0.51
coef_mix_KH = 0.33 !0.015, 0.4, 0.18, 0.33
coef_mix_hyp = 0.5 !0.05, 0.6, 0.25, 0.8
! non_avg = .true.
! deep_mixing = .true.
/

!-------------------------------------------------------------------------------
! wq setup
! if this block is read, water quality functionality will be enabled
!-------------------------------------------------------------------------------
! wq_lib [string]
! Select which WQ library to use;
! valid options are 'aed2' or 'fabm' [default is 'aed2']
! ode_method [integer]
! ODE numerical scheme for source and sink dynamics
! 1: first-order explicit (not positive)
! 2: second-order explicit Runge-Kutta (not positive)
! 3: fourth-order explicit Runge-Kutta (not positive)
! 4: Patankar (first-order, not conservative)
! 5: Patankar-RK (second-order, not conservative)
! 6: Patankar-RK (does not work, not conservative)
! 7: Modified Patankar (1st-order, conservat., posit.)
! 8: Modified Patankar-RK (2nd-order, conservat., posit.)
! 9: Modified Patankar-RK (does not work, conservat.,
! posit.)
! 10: Extended Modified Patankar (1st-order, conservat.,
! posit.)
! 11: Extended Modified Patankar-RK (2nd-order, conservat.,
! posit.)
! This variable is used only if bio_calc = True
! split_factor [integer, minimum = 1]
! number of biogeochemical time steps per physical time step
! bioshade_feedback [bool]
! feedback of bio-turbidity to temperature equation
! repair_state [bool]
! FABM option to repeair state variables that have -ve's
! wq_nml_file [string]
! name of .nml file to be passed to WQ library;
! the default is {wq_lib}.nml (eg aed2.nml)
! mobility_off [bool]
! flag to turn off settling/rising
! multi_ben [bool]
! GLM specific option for FABM to do benthic fluxes only
! in bottom layer, or on flanks of all layers (.true.)
!-------------------------------------------------------------------------------
&wq_setup
wq_lib = 'aed2'
wq_nml_file = 'aed2.nml'
ode_method = 1
split_factor = 1
!bioshade_feedback = .true.
bioshade_feedback = .false.
repair_state = .true.
! mobility_off = .false.
multi_ben = .true.
/

!-------------------------------------------------------------------------------
! lake details
!-------------------------------------------------------------------------------
!
! name [string]
! name of the lake
! latitude [float, minimum = -90, maximum = 90, unit = deg North]
! latitude
! longitude [float, minimum = -360, maximum = 360, unit = deg East]
! longitude
! base_elev [float]
! base elevation (m)
! crest_elev [float]
! crest elevation (m)
! bsn_len [float]
! basin length at crest (m)
! bsn_wid [float]
! basin width at crest (m)
! bsn_vals [integer]
! number of depth points on height-area relationship
! H [float]
! elevations (m) (comma separated list, len=bsn_vals)
! A [float]
! area (m2) (comma separated list, len=bsn_vals)
!
!-------------------------------------------------------------------------------
&morphometry
lake_name = 'Falling Creek'
latitude = 37.307681
longitude = -79.837068
bsn_len = 711.699
bsn_wid = 226.030
bsn_vals = 31
! H(m) A(m2) V(m3)
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
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
/

!-------------------------------------------------------------------------------
! duration of run
!-------------------------------------------------------------------------------
!
! timefmt [integer]
! method to specify start and duration of model run
! 1: duration computed from number of time steps, MaxN (bogus start
! date used) [no longer implemented!!]
! 2: duration computed from given start and stop dates (number of time
! steps MaxN computed)
! 3: duration computed from number of time steps, MaxN (start date as
! specified, stop date computed)
! start [string, format = "yyyy-mm-dd hh:mm:ss"]
! nominal start date
! This variable is used only if timefmt != 1
! stop [string, format = "yyyy-mm-dd hh:mm:ss"]
! nominal stop date
! This variable is used only if timefmt = 2
! dt [float, minimum = 0.001, maximum = 86400, unit = s]
! Time step for integration
! numb_days [number of days to run the simulation ]
! This variable is used only if timefmt != 2
!
!-------------------------------------------------------------------------------
&time
timefmt = 2
start = '2015-03-31 11:00:00'
stop = '2015-09-30 00:00:00'
dt = 3600.0
!num_days = 3288
timezone = -5.0
/

!-------------------------------------------------------------------------------
! format for output and filename(s)
!-------------------------------------------------------------------------------
!
! out_dir [string]
! path to output directory (set permissions)
! out_fn [string]
! name of output netcdf file
! nsave [integer, minimum = 1, maximum = 86400]
! save results every 'nsave' timesteps
! csv_lake_fname [string]
! name of lake.csv lake simulation daily summary information
! csv_point_nlevs [integer]
! number of depths at which to dump a csv time-series file
! csv_point_at [real]
! height from bottom for point csv file(s) (comma separated list)
! csv_point_fname [string]
! name of csv output file(s) (comma separated list)
! csv_point_nvars [integer]
! number of variables to output into csv
! csv_point_vars [string]
! list of names of variables to output, - order IS important
! csv_outlet_allinone [bool]
! put all outflow data into the same csv file
! csv_outlet_fname [string]
! name of csv output file(s) (comma separated list)
! csv_outlet_nvars [integer]
! number of variables to output into outlet csv
! csv_outlet_vars [string]
! list of names of variables to output
! csv_ovrflw_fname [string]
! name of csv file to record amount and quality of overflow
!
!-------------------------------------------------------------------------------! simulation number 1
&output
out_dir = '.'
out_fn = 'output'
nsave = 24
csv_point_nlevs = 2
csv_point_fname = 'WQ_'
csv_point_at = 20,22
csv_point_nvars = 6
csv_lake_fname = 'Physics'
csv_point_vars = 'temp','OXY_oxy','PHY_CYANOPCH1','PHY_CYANONPCH2','PHY_CHLOROPCH3','PHY_DIATOMPCH4'
/
!-------------------------------------------------------------------------------
! initial condition profiles
!-------------------------------------------------------------------------------
!
! lake_depth [float] initial lake depth (m)
! num_depths [integer] number of depths provided for initial profiles
! the_depths [float] the depths of the initial profile points (m)
! the_temps [float] the temperature of the initial profile points (C)
! the_sals [float] the salinity of the initial profile points (psu)
! num_wq_vars [integer] number of non GLM (ie FABM) vars to be initialised
! wq_names [string] names of non GLM (ie FABM) vars to be initialised
! wq_init_vals [float] array of FABM vars (rows = vars; cols = depths)
!
!-------------------------------------------------------------------------------
&init_profiles
num_depths = 30
lake_depth = 9.3
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,
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,
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
num_wq_vars = 7
wq_names =
'OGM_doc',
'OXY_oxy',
'CAR_dic',
'NIT_amm',
'NIT_nit',
'PHS_frp',
'CAR_ch4'
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,
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,
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,
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,
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,
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,
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
/
!-------------------------------------------------------------------------------
! meteorology
!-------------------------------------------------------------------------------
!
! met_sw [bool] switch to include surface meteorological forcing
! lw_type [string] type of longwave data supplied (LW_IN/LW_CC/LW_NET)
! rain_sw [bool] include rainfall nutrient composition
! snow_sw [bool] include snowfall (m/d)
! atm_stab [bool] account for non-neutral atmospheric stability
! catchrain [bool] flag that enables runoff from exposed banks of lake area
! rad_mode [integer] short and long wave radation model configuration (see manual)
! albedo_mode [integer] shortwave albedo calculation method
! cloud_mode [integer] atmospheric emmisivity calculation method
!
! meteo_fl [string] name of file with meteorology input data
! wind_factor [float] wind multiplication factor (-)
! wind_factor [float] wind multiplication factor (-)
! rain_factor [float] wind multiplication factor (-)
! sw_factor [float] wind multiplication factor (-)
! lw_factor [float] wind multiplication factor (-)
! at_factor [float] wind multiplication factor (-)
! rh_factor [float] wind multiplication factor (-)
!
! ce [float] bulk aerodynamic coefficient for latent heat transfer
! ch [float] bulk aerodynamic coefficient for sensible heat transfer
! cd [float] bulk aerodynamic coefficient for transfer of momentum
! rain_threshold [float] rainfall amount (m) required before runoff from exposed banks
! runoff_coef [float] conversion of rainfall to runoff in exposed lake banks
!
!-------------------------------------------------------------------------------
&meteorology
met_sw = .true.
lw_type = 'LW_IN'
rain_sw = .false.
snow_sw = .false.
atm_stab = .false.
catchrain = .false.
rad_mode = 1
albedo_mode = 1
cloud_mode = 4
!-- BC file details
meteo_fl = 'glm_met_2015_FCR_adjusted_tillDec.csv'
!meteo_fl = 'glm_met_2015_FCR_adjusted_wind.csv'
subdaily = .true.
wind_factor = 1.0
sw_factor = 1.0
lw_factor = 1.0
at_factor = 1.0
rh_factor = 1.0
rain_factor = 1.0
cd = 0.001
ce = 0.0013
ch = 0.0013
rain_threshold = 0.01
runoff_coef = 0.3
time_fmt = 'YYYY-MM-DD hh:mm:ss'
/
!-------------------------------------------------------------------------------
! inflows
!-------------------------------------------------------------------------------
!
! num_inflows [integer] number of inflowing streams (0+)
! names_of_strms [string] names of streams (comma separated list)
! strm_hf_angle [float] stream half angle (degrees)
! strmbd_slope [float] streambed slope (degrees)
! strmbd_drag [float] streambed drag coefficient (-)
! inflow_factor [float] inflow flow rate multiplier (-)
! inflow_fl [string] inflow data filename(s) (comma separated list)
! inflow_varnum [integer] number of columns (excluding date) to be read
! inflow_vars [string] variable names of inflow file columns
! This should be a comma separated list, and must
! include FLOW, SALT & TEMP (for GLM), and
! optionally can include FABM var names.
! coef_inf_entrain [real] entrainment coefficient for inflows
!
!-------------------------------------------------------------------------------
&inflow
num_inflows = 2
names_of_strms = 'river1','SSS'
subm_flag = .false.,.true.
strm_hf_angle = 100.0,35.0 !Degree of channelization
strmbd_slope = 0.573,0.1 !0.03-0.05 FCR inflow 0.03 SSS
strmbd_drag = 0.0160,0.0160
inflow_factor = 1,0.00314 !SSS 0.00314
inflow_fl = 'FCR_GLM_iof_2015_modified_9Jan17.csv','FCR_GLM_SSSin_2015_004.csv'
inflow_varnum = 10
inflow_vars = 'FLOW',
'TEMP',
'SALT',
'OGM_doc',
'NIT_amm',
'OXY_oxy',
'NIT_nit',
'PHS_frp',
'TOT_tn',
'TOT_tp'
/
!-------------------------------------------------------------------------------
! outflows
!-------------------------------------------------------------------------------
!
! num_outlet [integer] no. of outlets
! flt_off_sw [bool] floating offtake switches
! outl_elvs [float] outlet elevations (comma separated list)
! bsn_len_outl [float] basin length at outlets (m)
! bsn_wid_outl [float] basin width at outlets (m)
! outflow_fl [string] outflow data file
! outflow_factor [float] outflow flow rate multiplier (-)
! seepage [bool] do seepage processing [default is off - ie no seepage]
! seepage_rate [float] seepage rate of water (m/day) from bottom layer
!
!-------------------------------------------------------------------------------
&outflow
num_outlet = 4
flt_off_sw = .false.,.false.,.false.,.false.
outl_elvs = 506.9,498,506.9,506.9
bsn_len_outl = 711.699,100,711.699,711.699 !711.699
bsn_wid_outl = 226.030,10,226.030,226.030 !226.030
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'
outflow_factor = 1,0.00314,1,1 ! inflow 0.3
/
4 changes: 4 additions & 0 deletions tests/testthat/test-get_outputNC.R
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Expand Up @@ -17,6 +17,10 @@ test_that("get_wind", {
expect_true(all(t_out == df[,1]))
})

test_that("check hanging nml", {
expect_error(read_nml(system.file(package='glmtools', 'extdata', 'hanging_line.nml')), "Empty values after")
})

context("get_surface_height")

test_that("get_surface_height", {
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