manlaya/pymarthe-am

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Introduction

PyMarthe (v1.0) is a python wrapper acting as a "coupling interface" between MARTHE (v7.5) hydrogeological numerical models (BRGM) and optimization algorithms provided by the PEST++ facilities.

Documentation

PyMarthe classes and function documentation in English can be found here

Users are also invited to read the PyMarthe user manual (in French) and examples provided as Jupyter notebooks in this repository.

Getting Started

Load/manage MARTHE model

# -- Import usefull packages
import os, sys
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from pymarthe import MartheModel

# -- Load MARTHE Model
mm = MartheModel('mona.rma', spatial_index=True)

# -- Load non distributed properties
mm.load_prop('aqpump')  # aquifer pumping
mm.load_prop('soil')    # soil properties

# -- Load hydraulic distributed properties
hprops = ['permh', 'emmca', 'emmli', 'kepon']
for hprop in hprops:
    mm.load_prop(hprop)

# -- Extract field data (filtering)
mm.prop['permh'].get_data(layer=[4,5,6])

# -- Extract field data (sampling)
mm.prop['permh'].sample(x = [323.1,333.4],
                        y = [277.11,289.3],
                        layer = 4)

# -- Modify/Write field values
mm.prop['permh'].set_data(2.3e-3, layer=2, inest=0)
mm.prop['permh'.write_data()

# -- Plot field values
plt.rc('font', family='serif', size=8)
fig, ax = plt.subplots(figsize=(10,6))
extent = (300,205,490,380)
ax = mf.plot(ax=ax, layer=6, log=True,
             extent= extent, edgecolor='black', 
             lw=0.3, cmap='jet', zorder=10)
ax.set_title('MONA - Permeability (layer = 6)',
             fontsize = 12, fontweight="bold")

Run MARTHE model

# -- Make silent run
mm.remove_autocal()
mm.make_silent()
mm.run_model(exe_name='Marth_R8', verbose=False)

PEST interfacing

# -- Build optimisation
from pymarthe import MartheOptim
from pymarthe.utils import pest_utils

dirs = {f'{f}_dir': f for f in ['par', 'tpl', 'ins', 'sim'] }
mopt = MartheOptim(mm, name='mona_opt',**dirs)

# -- Add observations
for obsfile in os.listdir(dirs['obs_dir']):
    mopt.add_obs(data = obsfile, datatype='head')

# -- Add list-like parameters (based on KeysMultiIndex)
pump_kmi = pest_utils.get_kmi(mobj = mm.prop['aqpump'],
                              keys = ['boundname', 'layer', 'istep'])

mopt.add_param(parname = 'pumping',
               mobj = mm.prop['aqpump'],
               kmi = pump_kmi,
               value_col = 'value')

soil_kmi = pest_utils.get_kmi(mobj = mm.prop['soil'],
                              keys = ['soilprop', 'zone'])

mopt.add_param(parname = 'soil',
               mobj = mm.prop['soil'],
               kmi = soil_kmi,
               value_col = 'value')

# -- Add array-like parameters (based on izone)
mopt.add_param(parname='cf', mobj=mm.prop['emmca'],
               izone=None, pp_data=None,
               trans='log10', btrans='lambda x: 10**x',
               parlbnd=1e-15, parubnd=1e1, defaultvalue=1e-5) 



# -- Manage transformations
mopt.set_obs_trans(trans = 'log', datatype = 'head')
mopt.set_param_trans(trans = 'lambda x: np.log10(-x + 1)',
                     btrans = 'lambda x: - np.power(10, x) + 1',
                     parname= 'pumping')

# -- Write PEST files
mopt.write_insfile()
mopt.write_simfile()
mopt.write_parfile()
mopt.write_tplfile()

# -- Save parametrization (for forward run usage)
mopt.write_config()

# -- Build Pest Control File (.pst)
pst = mopt.build_pst(add_reg0= True,
                     write_pst= True,
                     write_config= True,
                     write_fr= True,
                     noptmax=0,
                     phimlim=5)

Contributing

Bug reports, code contributions, or improvements to the documentation are welcome from the community. Feel free to suggest improvements by working with your own fork version of PyMarthe. Go to the PyMarthe project page and hit the Fork button. You will want to clone your fork to your machine:

git clone <url_pymarthe> <pymarthe-yourname>
cd pymarthe-yourname

Ressources

• MARTHE - online documentation
• MARTHE - online User Guide
• PEST++ - GitHub page
• PEST - homepage
• pyEMU - GitHub page

Disclaimer

This software is experimental and is subject to revision.