{"id":39945396,"url":"https://github.com/daavid00/py-micp","last_synced_at":"2026-01-18T19:47:35.242Z","repository":{"id":151290661,"uuid":"444088296","full_name":"daavid00/py-micp","owner":"daavid00","description":"Open-source code to perform studies of MICP treatment and CO2 assessment.","archived":false,"fork":false,"pushed_at":"2025-12-03T15:16:40.000Z","size":5233,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-06T19:56:13.314Z","etag":null,"topics":["mrst","opm","porous-media-flow","python"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/daavid00.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":"SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-01-03T14:21:57.000Z","updated_at":"2025-12-03T15:13:51.000Z","dependencies_parsed_at":"2023-04-14T15:46:58.902Z","dependency_job_id":null,"html_url":"https://github.com/daavid00/py-micp","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/daavid00/py-micp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/daavid00%2Fpy-micp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/daavid00%2Fpy-micp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/daavid00%2Fpy-micp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/daavid00%2Fpy-micp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/daavid00","download_url":"https://codeload.github.com/daavid00/py-micp/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/daavid00%2Fpy-micp/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28549722,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T19:22:41.102Z","status":"ssl_error","status_checked_at":"2026-01-18T19:22:26.310Z","response_time":98,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["mrst","opm","porous-media-flow","python"],"created_at":"2026-01-18T19:47:34.518Z","updated_at":"2026-01-18T19:47:35.236Z","avatar_url":"https://github.com/daavid00.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://github.com/daavid00/py-micp/actions/workflows/CI.yml/badge.svg)](https://github.com/daavid00/py-micp/actions/workflows/CI.yml)\n\u003ca href=\"https://www.python.org/\"\u003e\u003cimg src=\"https://img.shields.io/badge/python-3.8%20to%203.14-blue.svg\"\u003e\u003c/a\u003e\n[![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![DOI](https://zenodo.org/badge/444088296.svg)](https://doi.org/10.5281/zenodo.16880620)\n\u003cimg src=\"py-micp.gif\" width=\"830\" height=\"250\"\u003e\n\n# py-micp: An Open-Source Simulation Workflow for Field-Scale Application of Microbially Induced Calcite Precipitation Technology for Leakage Remediation\n\nThis repository contains runscripts to simulate microbially induced calcite\nprecipitation (MICP) treatment in different domains; in addition to CO2 injection\nassessment in leakage paths before and after MICP application. We refer to \n[this paper](https://doi.org/10.1016/j.ijggc.2021.103256) for an extended description of the mathematical model.\n\nThe numerical examples accompanying this module are:\n* full_diagonal_leak,\n* full_double_leak,\n* full_single_leak,\n* quarter_diagonal_leak,\n* quarter_double_leak,\n* quarter_single_leak,\n* top_vs_vertical_variable_injection, and\n* towards_more_optimal_injection_strategies.\n\nThe scripts in these examples can be easily modified to run different studies\nchanging input parameter values, spatial domain properties, and implemented\nmodels in OPM Flow.\n\n## Installation\nYou will first need to install/download\n* [Flow](https://opm-project.org) (tested with Flow==2025.10)\n* [Python](https://www.python.org/downloads/) (tested with Python==3.14)\n* [GNU Octave](https://www.gnu.org/software/octave/download) (tested with GNU Octave==10.3.0)\n* [MRST](https://www.sintef.no/projectweb/mrst/download/) (tested with MRST==2025a)\n\nYou will also need to install some python packages, see ```requirements.txt``` \nfor a complete list. You can install all the required python packages in a \nvirtual environment with the following commands:\n\n```bash\n# Clone the repo\ngit clone https://github.com/daavid00/py-micp.git\n# Get inside the folder\ncd py-micp\n# Create virtual environment\npython3 -m venv vpy-micp\n# Activate virtual environment\nsource vpy-micp/bin/activate\n# Upgrade pip and setuptools\npip install --upgrade pip setuptools wheel\n# Install the python requirements\npip install -r requirements.txt\n```\n\nSee this [_installation_](https://opm.github.io/pyopmspe11/installation.html#opm-flow) for further details on building OPM Flow from the master branches in Linux, Windows (via [_WSL_](https://learn.microsoft.com/en-us/windows/wsl/)), and macOS.\n\nOnce you have installed OPM Flow, GNU Octave, and downloaded MRST:\n\n* Edit line 11 of the python scripts (e.g., 'quarter_single_leak.py') with the\nfull path to your 'flow' executable (e.g., '/Users/dmar/opm/build/opm-simulators/bin/flow') and simulator flags.\n\n* Edit line 2 of the GNU Octave scripts (e.g., 'quarter_single_leak.m') with the\nfull path to your MRST 'startup.m' file (e.g., '/Users/dmar/mrst-2025a/startup.m').\n\nTip: See the [CI.yml](https://github.com/daavid00/py-micp/blob/main/.github/workflows/CI.yml) for installation of \nall dependencies in Ubuntu 24.04 and running the test in _py-micp_.\n\n## Running the scripts\n* From the terminal, e.g., for the quarter_single_leak system:\n\n`python3 quarter_single_leak.py`\n\n## Citing\n* Landa-Marbán, D. 2025. py-micp: Open-source code to perform studies of MICP treatment and CO2 assessment. https://doi.org/10.5281/zenodo.16880621.\n\n## Publication\nThe following is a manuscript in which _py-micp_ is used:\n\n1. Tveit, S. and Landa-Marbán, D., 2022. Field-scale optimization of injection\nstrategies for leakage mitigation using microbially induced calcite\nprecipitation. https://arxiv.org/abs/2201.00669\n\nRefer to the [_v2024.10 release_](https://github.com/daavid00/py-micp/releases/tag/v2024.10) for the code that was used in that paper. This is relevant \nsince in the OPM Flow version 2025.04, the MICP implementation was refactored, resulting in changes in the deck keywords (e.g., now we use `BIOFPARA` instead \nof `MICPPARA`); see the corresponding OPM Flow version of the [_OPM Flow manual_](https://opm-project.org/?page_id=955) for details.\n\n## About py-micp\nThe _py-micp_ package was funded by the [_Efficient models for microbially induced calcite precipitation as a seal for CO2 storage (MICAP) project_](https://gassnova.no/app/uploads/sites/4/2022/02/Sluttrapport-MICAP.pdf) [project number 268390].\nContributions are more than welcome using the fork and pull request approach.\nFor new features, please request them raising an issue.\n\n## Related\nBelow are some tools that might be of interest; check ‘em out 🙂.\n\n* ad-micp: A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP) (https://github.com/daavid00/ad-micp).\n* pyopmspe11: A Python framework using OPM Flow for the CSP SPE11 benchmark project (https://github.com/OPM/pyopmspe11).\n* pycopm: An open-source tool to tailor OPM Flow geological models (https://github.com/cssr-tools/pycopm).\n* plopm: Quick generation of PNGs, GIFs, and VTKs from a OPM Flow type model (https://github.com/cssr-tools/plopm).\n* pofff: An open-source image-based history-matching framework for the FluidFlower benchmark study using OPM Flow (https://github.com/cssr-tools/pofff).\n* pyopmnearwell: A Python framework to simulate near well dynamics using OPM Flow (https://github.com/cssr-tools/pyopmnearwell).\n* expreccs: A Python framework using OPM Flow to simulate regional and site reservoirs for CO2 storage (https://github.com/cssr-tools/expreccs).\n* pymm: An open-source image-based framework for CFD in microsystems (https://github.com/cssr-tools/pymm).\n\n## Contact\nDavid Landa-Marbán (dmar@norceresearch.no).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdaavid00%2Fpy-micp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdaavid00%2Fpy-micp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdaavid00%2Fpy-micp/lists"}