diff --git a/docs/source/_resources/joss/figures/figures.py b/docs/source/_resources/joss/figures/figures.py index 8c341ef5..bfbb854f 100644 --- a/docs/source/_resources/joss/figures/figures.py +++ b/docs/source/_resources/joss/figures/figures.py @@ -47,7 +47,7 @@ elif _input_flag == 'plot': # set up attributes needed for plotting - H_SL, h, n = 0, 3, 0.3 # sea level, basin depth, surf relief + H_SL, h, n = 0, 4, 0.3 # sea level, basin depth, surf relief blues = matplotlib.cm.get_cmap('Blues_r', 64) greens = matplotlib.cm.get_cmap('YlGn_r', 64) combined = np.vstack((blues(np.linspace(0.1, 0.7, 5)), diff --git a/docs/source/_resources/joss/figures/pyDeltaRCM_20210810-151130.log b/docs/source/_resources/joss/figures/pyDeltaRCM_20210810-151130.log new file mode 100644 index 00000000..f63c4754 --- /dev/null +++ b/docs/source/_resources/joss/figures/pyDeltaRCM_20210810-151130.log @@ -0,0 +1,4072 @@ +2021-08-10 15:11:30,195 - INFO - Output log file initialized +2021-08-10 15:11:30,195 - INFO - pyDeltaRCM version 2.0.2 +2021-08-10 15:11:30,195 - INFO - Python version 3.9.5 (default, Jun 4 2021, 12:28:51) +[GCC 7.5.0] +2021-08-10 15:11:30,199 - INFO - Platform: Linux-5.11.0-25-generic-x86_64-with-glibc2.31 +2021-08-10 15:11:30,199 - INFO - Setting up model configuration +2021-08-10 15:11:30,199 - INFO - Model type is: DeltaModel +2021-08-10 15:11:30,199 - INFO - Configuration variable `out_dir`: /media/andrew/mass/Dropbox/software/deltarcm/pyDeltaRCM/docs/source/_resources/joss/figures +2021-08-10 15:11:30,199 - INFO - Configuration variable `verbose`: 0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `seed`: 10151919 +2021-08-10 15:11:30,200 - INFO - Configuration variable `Length`: 5000.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `Width`: 10000.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `dx`: 50.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `L0_meters`: 150.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `S0`: 0.00015 +2021-08-10 15:11:30,200 - INFO - Configuration variable `itermax`: 3 +2021-08-10 15:11:30,200 - INFO - Configuration variable `Np_water`: 2000 +2021-08-10 15:11:30,200 - INFO - Configuration variable `u0`: 1.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `N0_meters`: 250.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `h0`: 5.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `hb`: None +2021-08-10 15:11:30,200 - INFO - Configuration variable `H_SL`: 0.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `SLR`: 0.0 +2021-08-10 15:11:30,200 - INFO - Configuration variable `Np_sed`: 2000 +2021-08-10 15:11:30,200 - INFO - Configuration variable `f_bedload`: 0.5 +2021-08-10 15:11:30,200 - INFO - Configuration variable `active_layer_thickness`: None +2021-08-10 15:11:30,200 - INFO - Configuration variable `C0_percent`: 0.1 +2021-08-10 15:11:30,200 - INFO - Configuration variable `Csmooth`: 0.9 +2021-08-10 15:11:30,200 - INFO - Configuration variable `toggle_subsidence`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `subsidence_rate`: 2e-09 +2021-08-10 15:11:30,200 - INFO - Configuration variable `start_subsidence`: 216000 +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_eta_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_stage_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_depth_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_discharge_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_velocity_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_sedflux_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_sandfrac_figs`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_figs_sequential`: True +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_metadata`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_eta_grids`: True +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_stage_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_depth_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_discharge_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_velocity_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_sedflux_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_sandfrac_grids`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_discharge_components`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_velocity_components`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_dt`: 86400 +2021-08-10 15:11:30,200 - INFO - Configuration variable `checkpoint_dt`: None +2021-08-10 15:11:30,200 - INFO - Configuration variable `save_checkpoint`: False +2021-08-10 15:11:30,200 - INFO - Configuration variable `resume_checkpoint`: False +2021-08-10 15:11:30,201 - INFO - Configuration variable `omega_sfc`: 0.1 +2021-08-10 15:11:30,201 - INFO - Configuration variable `omega_flow`: 0.9 +2021-08-10 15:11:30,201 - INFO - Configuration variable `Nsmooth`: 10 +2021-08-10 15:11:30,201 - INFO - Configuration variable `theta_water`: 1.0 +2021-08-10 15:11:30,201 - INFO - Configuration variable `coeff_theta_sand`: 2.0 +2021-08-10 15:11:30,201 - INFO - Configuration variable `coeff_theta_mud`: 1.0 +2021-08-10 15:11:30,201 - INFO - Configuration variable `beta`: 3 +2021-08-10 15:11:30,201 - INFO - Configuration variable `sed_lag`: 1.0 +2021-08-10 15:11:30,201 - INFO - Configuration variable `coeff_U_dep_mud`: 0.3 +2021-08-10 15:11:30,201 - INFO - Configuration variable `coeff_U_ero_mud`: 1.5 +2021-08-10 15:11:30,201 - INFO - Configuration variable `coeff_U_ero_sand`: 1.05 +2021-08-10 15:11:30,201 - INFO - Configuration variable `alpha`: 0.1 +2021-08-10 15:11:30,201 - INFO - Configuration variable `stepmax`: None +2021-08-10 15:11:30,201 - INFO - Configuration variable `sand_frac_bc`: 0 +2021-08-10 15:11:30,201 - INFO - Configuration variable `clobber_netcdf`: False +2021-08-10 15:11:30,222 - INFO - Random seed is: 10151919 +2021-08-10 15:11:32,810 - INFO - Model initialization complete +2021-08-10 15:11:32,810 - INFO - Time: 0.0; timestep: 0 +2021-08-10 15:11:47,973 - INFO - Time: 25000.0; timestep: 1 +2021-08-10 15:11:51,027 - INFO - Time: 50000.0; timestep: 2 +2021-08-10 15:11:55,031 - INFO - Time: 75000.0; timestep: 3 +2021-08-10 15:11:59,147 - INFO - Time: 100000.0; timestep: 4 +2021-08-10 15:12:03,174 - INFO - Time: 125000.0; timestep: 5 +2021-08-10 15:12:07,664 - INFO - Time: 150000.0; timestep: 6 +2021-08-10 15:12:12,066 - INFO - Time: 175000.0; timestep: 7 +2021-08-10 15:12:16,713 - INFO - Time: 200000.0; timestep: 8 +2021-08-10 15:12:21,475 - INFO - Time: 225000.0; timestep: 9 +2021-08-10 15:12:25,962 - INFO - Time: 250000.0; timestep: 10 +2021-08-10 15:12:30,369 - INFO - Time: 275000.0; timestep: 11 +2021-08-10 15:12:34,545 - INFO - Time: 300000.0; timestep: 12 +2021-08-10 15:12:38,674 - INFO - Time: 325000.0; timestep: 13 +2021-08-10 15:12:42,681 - INFO - Time: 350000.0; timestep: 14 +2021-08-10 15:12:46,642 - INFO - Time: 375000.0; timestep: 15 +2021-08-10 15:12:50,255 - INFO - Time: 400000.0; timestep: 16 +2021-08-10 15:12:53,644 - INFO - Time: 425000.0; timestep: 17 +2021-08-10 15:12:57,064 - INFO - Time: 450000.0; timestep: 18 +2021-08-10 15:13:00,397 - INFO - Time: 475000.0; timestep: 19 +2021-08-10 15:13:03,645 - INFO - Time: 500000.0; timestep: 20 +2021-08-10 15:13:06,783 - INFO - Time: 525000.0; timestep: 21 +2021-08-10 15:13:09,734 - INFO - Time: 550000.0; timestep: 22 +2021-08-10 15:13:12,664 - INFO - Time: 575000.0; timestep: 23 +2021-08-10 15:13:15,586 - INFO - Time: 600000.0; timestep: 24 +2021-08-10 15:13:18,333 - INFO - Time: 625000.0; timestep: 25 +2021-08-10 15:13:20,965 - INFO - Time: 650000.0; timestep: 26 +2021-08-10 15:13:23,507 - INFO - Time: 675000.0; timestep: 27 +2021-08-10 15:13:26,295 - INFO - Time: 700000.0; timestep: 28 +2021-08-10 15:13:28,847 - 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This is useful to understand, for example, shifting delta morphology due to sea-level rise, changing vegetal cover, or flooding intensity. As a result, many numerical delta models have been proposed in the literature, and results from these studies are difficult to compare because of various design and implementation choices. -*pyDeltaRCM* (`v2.x`) delivers a computationally efficient and easy-to-customize implementation of the DeltaRCM numerical model [@liang_reduced_1_2015], enabling comparison and reproducibility in studies of delta change due to various environmental forcings. +*pyDeltaRCM* (`v2.0`) delivers a computationally efficient and easy-to-customize implementation of the DeltaRCM numerical model [@liang_reduced_1_2015], enabling comparison and reproducibility in studies of delta change due to various environmental forcings. # Statement of need @@ -44,20 +44,20 @@ For example, changes in sediment input to the delta modulate the rate at which n In addition to natural processes, human landscape modification renders deltaic environments more sensitive to global climate change into the future [@paola_natural_2011]. Demand to understand natural delta processes, and how these processes will respond to various environmental forcings, has led to a proliferation of numerical delta models in the literature [@overeem_three_2005]. -The DeltaRCM delta model [@liang_reduced_1_2015] has gained popularity among geomorphologists due to an attractive balance of computational cost, realism, and interpretability [@larsen_appropriate_2016]. +The DeltaRCM delta model [@liang_reduced_1_2015] has gained popularity among geomorphologists due to an attractive balance of computational cost, realism, and interpretability [@larsen_appropriate_2016]. For example, studies have employed the DeltaRCM design to examine delta morphology and dynamism response to sea-level rise and regional subsidence [@liang_quantifying_2016; @liang_how_2016], as well as extended model design to simulate delta evolution with vegetation [@lauzon_comparing_2018] and ice and permafrost [@lauzon_ice_2019; @piliouras_unraveling_2021]. However, comparison among these studies is difficult, owing to disparate code bases, various implementation choices, lack of version control, and proprietary software dependencies. # Background -Here, version 2.x of *pyDeltaRCM* is introduced; *pyDeltaRCM* is a computationally efficient, free and open source, and easy-to-customize numerical delta model based on the original DeltaRCM design. +Here, version 2.0 of *pyDeltaRCM* is introduced; *pyDeltaRCM* is a computationally efficient, free and open source, and easy-to-customize numerical delta model based on the original DeltaRCM design. The original DeltaRCM framework is inspired by well-understood physical phenomena, and models mass movement as a probabilistic weighted random-walk process coupled with a set of hierarchical rules; the model is extensively described in @liang_reduced_1_2015 and @liang_reduced_2_2015. -This same framework is the basis for *pyDeltaRCM* v2.x, with a few modifications selected only to resolve known numerical instabilities, improve computational efficiency, and support reproducible simulations. +This same framework is the basis for *pyDeltaRCM* v2.0, with a few modifications selected only to resolve known numerical instabilities, improve computational efficiency, and support reproducible simulations. *PyDeltaRCM* depends only on common Python packages `numpy` [@harris2020], `matplotlib` [@hunter2007], `scipy` [@virtanen2020], `netCDF4`, `pyyaml`, and `numba` [@lam_numba_2015]. -![Simulation with *pyDeltaRCM* v2.x, default parameter set, and random `seed: 10151919`. Simulation was run for 4000 timesteps, and assumes 10 days of bankfull discharge per year. \label{fig:timeseries}](figures/timeseries.png) +![Simulation with *pyDeltaRCM* v2.0, default parameter set, and random `seed: 10151919`. Simulation was run for 4000 timesteps, and assumes 10 days of bankfull discharge per year; computational time was \~2 hours. \label{fig:timeseries}](figures/timeseries.png) # Flexible and easy to use