{"id":46519232,"url":"https://github.com/gemshub/xgems","last_synced_at":"2026-03-06T19:02:02.115Z","repository":{"id":310971241,"uuid":"1033065535","full_name":"gemshub/xgems","owner":"gemshub","description":"This is a numerical solver of chemical equilibria for thermodynamic modelling, extended (relative to GEMS3K code) with new [C++ and Python APIs] ","archived":false,"fork":false,"pushed_at":"2025-11-27T07:59:16.000Z","size":37474,"stargazers_count":1,"open_issues_count":9,"forks_count":2,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-11-30T01:46:01.880Z","etag":null,"topics":["environmental","equilibrium","geochemical-modeling","geochemistry","gibbs-energy","kinetics","reactive-transport","sorption","thermodynamic"],"latest_commit_sha":null,"homepage":"https://xgems.readthedocs.io/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gemshub.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-08-06T08:47:37.000Z","updated_at":"2025-11-24T14:09:46.000Z","dependencies_parsed_at":"2025-08-21T11:45:16.530Z","dependency_job_id":null,"html_url":"https://github.com/gemshub/xgems","commit_stats":null,"previous_names":["gemshub/xgems"],"tags_count":17,"template":false,"template_full_name":null,"purl":"pkg:github/gemshub/xgems","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gemshub%2Fxgems","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gemshub%2Fxgems/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gemshub%2Fxgems/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gemshub%2Fxgems/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gemshub","download_url":"https://codeload.github.com/gemshub/xgems/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gemshub%2Fxgems/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30192367,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-06T18:54:55.862Z","status":"ssl_error","status_checked_at":"2026-03-06T18:53:04.013Z","response_time":250,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["environmental","equilibrium","geochemical-modeling","geochemistry","gibbs-energy","kinetics","reactive-transport","sorption","thermodynamic"],"created_at":"2026-03-06T19:01:54.571Z","updated_at":"2026-03-06T19:02:02.063Z","avatar_url":"https://github.com/gemshub.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n## xGEMS \n\nLinux, OSX, Windows\n\nThis is a numerical solver of chemical equilibria for thermodynamic modelling, extended (relative to GEMS3K code) with new [C++ and Python APIs](https://gemshub.github.io/site/start/gemstandalone/documentation/#cpython-chemicalengine-interface), and supposed to replace GEMS3K in next-generation software.  \n\n### Documentation\n\nFor detailed information about how to use this project through its C++ and Python interface interface [View Documentation](https://xgems.readthedocs.io)\n\n### Briefly about xGEMS\n\n* Currently uses the [GEMS3K](https://github.com/gemshub/GEMS3K) code that implements the improved GEM IPM-3 algorithm for Gibbs energy minimization in very complex non-ideal chemical systems with two-sided metastability constraints.\n* Written in C/C++. The xGEMS code can be compiled as a standalone program (see /demos); or built as a static or dynamic library for coupling with a mass transport simulator or another code.\n\n### License\n* GEMS3K is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\n* GEMS3K 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 Lesser General Public License for more details.\n* You should have received a copy of the GNU Lesser General Public License along with GEMS3K code. If not, see http://www.gnu.org/licenses/. \n\n### Installation using Conda \n\n[![Conda-Forge](https://img.shields.io/conda/vn/conda-forge/xgems?style=for-the-badge\u0026logo=conda-forge)](https://anaconda.org/conda-forge/xgems)\n\nxGEMS can be easily installed using [Conda](https://www.anaconda.com/docs/getting-started/miniconda/install) package manager. If you have Conda or Miniforge installed, first add the conda-forge channel by executing \n\n```bash\nconda config --add channels conda-forge\n```\n\ninstall xGEMS by executing the following command:\n\n```bash\nconda install xgems\n```\n\nConda can be installed from [Miniconda](https://conda.io/miniconda.html).\n\n### How to download xGEMS source code\n\n* In your home directory, make a folder named e.g. ~/git/xGEMS.\n* Change into ~/git/xGEMS and clone this repository from https://bitbucket.org/gems4/xgems.git using a preinstalled free git client, e.g. SourceTree. \n* Alternatively on Mac OS X or linux, open a terminal and type in the command line:\n```bash\ncd ~/git/xGEMS\ngit clone https://bitbucket.org/gems4/xgems.git .\n```\n\n### How to build xGEMS library and examples\n\n#### **Option 1: Build xGEMS in a Conda Environment Using `conda-devenv`**\n\n1. **Install Conda and `conda-devenv`**  \n   Ensure you have Conda installed. If not, download and install Miniconda or Anaconda from [here](https://docs.conda.io/en/latest/miniconda.html).  \n   Install `conda-devenv`:\n   ```bash\n   conda install -c conda-forge conda-devenv\n   ```\n\n2. **Create and Activate the Conda Environment** \n   ```bash\n   conda devenv\n   conda activate xgems\n   ```\n3. **Build xGEMS**\n   ```bash\n   cd ~/git/xGEMS\n   mkdir build\n   cd build\n   cmake .. -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX\n   make\n   make install\n   ```\n\n#### **Option 2: Build xGEMS without Conda**\n\n\n1. **Install Dependencies**\n\n   by executing in ```~/xGEMS$```\n   \n   ```bash\n   sudo ./install-dependencies.sh\n   ```\n\n2. **Build xGEMS** \n\n   To build xGEMS and install it in your home directory or in the system directory (as in the example below), a typical sequence of commands can be executed in the terminal:\n   \n   ```sh\n   cd ~/xGEMS\n   mkdir build\n   cd build\n   cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local\n   make\n   sudo make install\n   ```\n\n#### Verify installation\n\n   * To execute the c++ demo:\n   \n   ```bash\n   cd ~/build/bin\n   ./demo1\n   ```\n   \n   * To execute the python demo: \n   \n   ```bash\n    cd ~git/xGEMS/demos/\n    python3 demo1.py\n   ```\n\n## For developers\n\n### Update documentation \n\nInstall doxygen\n\n```bash\nsudo apt install doxygen  # Linux\n```\nInstall addons \n```bash\npip install sphinx breathe sphinx_rtd_theme\npip install sphinx-autodoc-typehints\npip install sphinxcontrib-autodoc-doxygen\n```\n\n(first build and install xgems, then update documentation)\n\nGenerate xml and html\n```bash\ndoxygen Doxyfile\nsphinx-build -b html docs/sphinx/source docs/html\n```\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgemshub%2Fxgems","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgemshub%2Fxgems","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgemshub%2Fxgems/lists"}