Plot subsurface variables

# # skip this if package has already been installed
# !pip install modvis

%matplotlib inline
%load_ext autoreload
%autoreload 2

import os
import numpy as np
import modvis.ats_xdmf as xdmf
import modvis.plot_vis_file as pv
import logging
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s: %(message)s')

work_dir = f"../../model2/"
run_dir = "3-transient"
model_dir = os.path.join(work_dir, run_dir)
logging.info(f"Loading data from {model_dir}")
# model_dir = "../data/coalcreek"

2025-04-07 15:02:18,146 - root - INFO: Loading data from ../../model2/3-transient

# import numpy as np
# import modvis.ats_xdmf as xdmf
# import modvis.plot_vis_file as pv

# model_dir = "../data/coalcreek"

Download the sample data when running on Google Colab

# import os
# if not os.path.exists(model_dir):
#   !git clone https://github.com/pinshuai/modvis.git
#   %cd ./modvis/examples/notebooks

import vis data

visfile = xdmf.VisFile(model_dir, domain=None, load_mesh=True, columnar=True, 
                      model_time_unit= 'd')

# all available variable names
list(visfile.d.keys())

['base_porosity',
 'capillary_pressure_gas_liq',
 'cell_volume',
 'darcy_velocity.0',
 'darcy_velocity.1',
 'darcy_velocity.2',
 'mass_density_liquid',
 'molar_density_liquid',
 'permeability',
 'plant_wilting_factor',
 'porosity',
 'pressure',
 'relative_permeability',
 'root_fraction',
 'saturation_gas',
 'saturation_liquid',
 'transpiration',
 'viscosity_liquid',
 'water_content',
 'water_source']

plot subsurface satuation

single column

This will print a variable across a single column over the entire simulation period. The user needs to provide cell ids associated with the column.

The cell ID can be found using ParaView with the following steps:

1. Load data into Paraview. Click apply

2. Click on SplitView icon and choose SpreadSheetView

3. Under SpreadSheetView, change Attribute to Cell Data; Toggle on Show only selected elements (next to the Precision)

4. Under RenderView, turn on Interactively select cells on

5. Select cells of interests and the spreadsheet will be auto populated the cell attributes with the first column being Cell ID

6. Provide the Cell ID in pv.plot_column_data().

fig, ax = pv.plot_column_data(visfile, var_name = "saturation_liquid", cmap = "coolwarm", 
                              cell_id = 23316, infer_col_from_cell=True)

single layer

time_slice = '2016-6-10'

fig, ax = pv.plot_layer_data(visfile, var_name = "saturation_liquid", 
                             layer_ind = 9, time_slice= time_slice,
                          cmap = "coolwarm")

plot groundwater table

single column

ihead = pv.plot_column_head(visfile, cell_id = 22903, infer_col_from_cell=True)

GW surface

fig, ax, tpc = pv.plot_gw_surface(visfile, contour = True, 
                                  contourline = True, nlevel = np.arange(2700,3665, 50), 
                                  colorbar = True,
                                  time_slice = time_slice, 
                                 )

Volumetric water content

fig, ax, tpc = pv.plot_water_content(visfile, layer_ind = 0, 
                                     vmin = 0.1, vmax = 0.22, cmap = 'turbo',
                                     time_slice=time_slice)