remappy 0.0.0.5

Reaction-Transport Modeling in Porous Media

Overview

REMAP (Chernyavsky & Wortmann, 2007, DOI 10.1029/2006GC001442) provides an easy to use interface for 1-dimensional reaction-transport modeling in porous media, and provides explicit support for kinetic stable isotope fractionation calculations.

The original program was written as matlab program. Remappy provides a python wrapper to the original code which can be run via oct2py.

News:

• April 5^th: v 0.0.0.4, installation path is now updated during installation, non-python files are now included in installation script. Updated installation instructions
• March 30^th: Initial release

Installation

• pip install remappy will install all necessary files and dependencies
• you can now import remap into your python code (see below)
• to run remap as standalone application, you need to follow your os specific instructions to create an executable python program. On linux, it is sufficient to link remap.py to a directory which is in your path (often /usr/local/bin/) and set is a executable. Tools like https://datatofish.com/executable-pyinstaller/ will also work on Mac and Windows.

Usage

• remap.py: This behaves similar to the original remap but provides extended command-line parsing options, run remap.py --help for details
• you can also import the library and use it inside of your own python code

import remap
import pathlib as pl
import pandas as pd

fn: str = "hg.rmp"  # remap config file
cwd: pl.Path = pl.Path.cwd()  # get the current working directory
fqfn: pl.Path = pl.Path(f"{cwd}/{fn}")  # fully qualified file name

if not fqfn.exists():  # check if file exist
    raise FileNotFoundError(f"Cannot find file {fn}")

# run remap and return results as dataframe
df: pd.DataFrame = remap.run_remap(str(fname))

• or use the oct2py interface directly

from oct2py import octave

octave.addpath("/path/to/remap.m")

fn = "hg.rmp"  # name of remap configuration file
# call remap
[c, conc, r, v, par] = octave.start_remap(fn, nout=5)

Documentation

See the docs folder for the original REMAP documentation.

Todo

• port more matlab code to python
• provide more examples
• do more testing

License

remappy: reaction-transport modeling Copyright (C), 2022 Ulrich G. Wortmann

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.