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@@ -4,19 +4,52 @@ A generalized python library for calculating and plotting various things related | |
| [](https://vesical.readthedocs.io/en/latest/?badge=latest) | ||
| [](https://doi.org/10.5281/zenodo.5095382) | ||
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| ## Use VESIcal online with no installation | ||
| Use VESIcal in Binder! | ||
| ## Documentation | ||
| Check here first for all your VESIcal questions! And be sure to read the manuscripts. | ||
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| - Read all of our documentation, inlcuding quickstart guides here: https://vesical.readthedocs.io/en/latest/ | ||
| - Check our our YouTube channel for videos on how to use VESIcal here: https://www.youtube.com/channel/UCpvCCs5KMXzOxXWm0seF8Qw | ||
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| ### Interactive versions of manuscripts | ||
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| - Direct link to interactive VESIcal Part I manuscript: [](https://mybinder.org/v2/gh/kaylai/vesical-binder/HEAD?filepath=Manuscript.ipynb) | ||
| - Jupyter Notebook hub with VESIcal: [](https://mybinder.org/v2/gh/kaylai/vesical-binder/HEAD) | ||
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| ### PDF versions of manuscripts | ||
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| - [VESIcal Part I: An Open-Source Thermodynamic Model Engine for Mixed Volatile (H2O-CO2) Solubility in Silicate Melts](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020EA001584) | ||
| - [VESIcal Part II: A critical approach to volatile solubility modelling using an open-source Python3 engine](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021EA001932) | ||
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| ## Installation and online use | ||
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| In general, VESIcal can be accessed and used in a variety of ways. From most flexible (advanced) to least flexible (novice), these are: | ||
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| **Direct link to manuscript:** | ||
| [](https://mybinder.org/v2/gh/kaylai/vesical-binder/HEAD?filepath=Manuscript.ipynb) | ||
| - local installation of the VESIcal library | ||
| - through the ENKI server (recommended for most users) | ||
| - through a [jupyter notebook version of the VESIcal manuscript](https://mybinder.org/v2/gh/kaylai/vesical-binder/HEAD?filepath=Manuscript.ipynb). | ||
| - via the web-app [https://vesical.anvil.app/](https://vesical.anvil.app/) | ||
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| **Jupyter Notebook hub with VESIcal:** | ||
| [](https://mybinder.org/v2/gh/kaylai/vesical-binder/HEAD) | ||
| ### VESIcal on the ENKI server | ||
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| VESIcal requires installation of not only the VESIcal library but also some other python libraries, one of which is a bit tricky to install (ENKI/thermoengine aka the engine behind MELTS). But, we have a solution! All dependencies and the latest version of VESIcal are all installed on the ENKI server, within a Jupyter Notebook Hub. Steps to use VESIcal on the ENKI server are: | ||
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| ## Installation | ||
| 1. Create a (free) GitLab account, which you'll use to sign into ENKI here: https://gitlab.com/users/sign_up | ||
| 2. Email ENKI PI Mark Ghiorso at [email protected] with your GitLab username and requet access to the ENKI server. | ||
| 3. Access the ENKI Production Server by going to http://enki-portal.org/ and clicking "SERVERS" > "PRODUCTION SERVER" | ||
| 4. Sign in with your GitLab credentials: You are now in your own jupyter notebook workspace! You can upload and create files here. They won't be accessible to anyone else. | ||
| 5. Click the green "CLOSE THIS SCREEN" button | ||
| 6. Create a new notebook by clicking the blue plus button and then selecting Python3 under Notebook. Or select from the menu File > New > Notebook | ||
| 7. Be sure to import VESIcal as v at the top of your file, and now you are ready to get to work! | ||
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| First, obtain Python3.x if you do not already have it installed. If you are new to python, we recommend installing it via anaconda3 (https://www.anaconda.com/products/individual). VESIcal can be installed with one line. Open a terminal and type the following: | ||
| See video tutorials on our ReadTheDocs page for more. | ||
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| ### Installing locally | ||
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| **Important! Thermoengine must be installed!** | ||
| Please see below for details on how to install thermoengine, the python implementation of MELTS/MagmaSat | ||
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| First, obtain Python3.x if you do not already have it installed. If you are new to python, we recommend installing it via [anaconda3](https://www.anaconda.com/products/individual). VESIcal can be installed with one line. Open a terminal and type the following: | ||
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| ``` | ||
| pip install VESIcal | ||
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| If any warnings related to these libraries appear, try installing them as you did VESIcal: with 'pip install [package]'. | ||
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| thermoengine is the ENKI implementation of MELTS (MagmaSat), which is the backbone of the entire VESIcal library. VESIcal cannot be run without thermoengine at this time, however a VESIcal-lite that does not include MagmaSat is planned. To install thermoengine, please refer to the ENKI documentation here: https://gitlab.com/ENKI-portal/ThermoEngine. | ||
| ### Installing thermoengine | ||
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| ## Documentation | ||
| Read all of our documentation, inlcuding quickstart guides here: https://vesical.readthedocs.io/en/latest/ | ||
| Thermoengine is the ENKI implementation of MELTS (MagmaSat), which is the default solubility model implemented in VESIcal. VESIcal cannot be run without thermoengine at this time, however a VESIcal-lite that does not include MagmaSat is planned. To install thermoengine, please refer to the ENKI documentation here: https://gitlab.com/ENKI-portal/ThermoEngine. | ||
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| In almost all cases you will need to install thermoengine using docker. The thermoengine devs have kindly put together a docker image for you. We suggest you follow those instructions here: https://gitlab.com/ENKI-portal/ThermoEngine/-/tree/master/#running-a-container-image-locally. | ||
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| Check our our YouTube channel for videos on how to use VESIcal here: https://www.youtube.com/channel/UCpvCCs5KMXzOxXWm0seF8Qw | ||
| ## Updating | ||
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| To upgrade to the most recent version of VESIcal, type the following into terminal: | ||
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| ``` | ||
| pip install VESIcal --upgrade | ||
| ``` | ||
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| ## Contributing | ||
| Issues are tracked on [GitHub](https://github.com/kaylai/VESIcal/issues). | ||
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