GibbsTS 1.0.4

GTS: An automated toolkit for building Gibbs thermodynamic surface with application to obtain high-pressure melting data.

GTS: Gibbs Thermodynamic Surface

Overview

GTS: Gibbs Thermodynamic Surface is an automated toolkit designed for efficiently obtaining high-pressure melting data, including melting points and thermodynamic potentials of materials. By constructing the Gibbs thermodynamic surface using a geometrical method, it provides fast and accurate calculations for both solid and liquid phases.

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Features

• Automated surface generation: Builds thermodynamic surfaces for solid and liquid phases.
• Melting data: Obtaining melting data for solid and liquid phases based on user-defined pressure conditions. With the ab initio molecular dynamics (AIMD) simulation data in the NVT (N, number of atoms; V, volume; T, temperature) ensemble and the reference point, GTS is able to rapidly present melting data, including volume, pressure, temperature, and thermodynamic potentials
• A reference point: Comparing the traditionally-used Clausius-Clapeyron integration (CCI) method with our GTS approach, the same thing is that a reference melting point is needed.

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Installation

Installing GTS in a Python 3 environment is straightforward. We recommend two ways to install GTS:

From PyPI

You can install GTS directly from PyPI: pip install GibbsTS

From Source

1. Clone the repository:

   git clone https://github.com/computation-mineral-physics-group/GTS.git
   cd GTS
   

2. Install dependencies:

   pip install -r requirements.txt
   

3. Install GTS:

   pip install .
   

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Run

GTS provides two primary functions: building the Gibbs thermodynamic surface and calculating melting data. These functionalities can be accessed via a command-line interface.

Input Files

It is of great importance to prepare two files before running: {name}_solid_input.txt, {name}_liquid_input.txt.

Command For Running

Argument	Type	Default	Description
-n, --name	str	None	The name of the material for which you want to obtain melting data.
-s, --surface	bool	False	Build the Gibbs thermodynamic surface and store its data in [name].json.
-mtr, --melt_temp_refer	float	0	The reference melting temperature (unit: K).
-mpr, --melt_pressure_refer	float	0	The reference melting pressure (unit: GPa).
-p, --pressure	float	0	The target pressure for melting point calculation (unit: GPa).
-i, --image	bool	False	Save the G-T plot indicating the melting point.
-u, --unit	str	internal	Units defined by the user. (e.g., vasp or internal).
-min, --minpressure	float	0	Lower limit of the pressure range (in GPa).
-max, --maxpressure	float	0	Upper limit of the pressure range (in GPa).
-num, --number	float	6	Number of melting points to compute over the pressure range.
-d, --debug	bool	False	Enable debug mode.
-v, --version	flag	VersionAction	Show the program's version.

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Example Usage

1. Generate Thermodynamic Surface

Run the following command to generate the Gibbs thermodynamic surface for the target material and store the data in [name].json:

GTS -n [name] -s -mtr [value] -mpr [value]

2. Obtain Melting Data

This command will output melting point at the user-defined pressure and its thermodynamic potentials for the two phases (solid phase and liquid phase) in the terminal.

GTS -n [name] -p [value] -u [type] -i

This command will output the diagrams of thermodynamic potentials over the user-defined pressure range.

GTS -n [name] -min [value] -max [value]

3. Debug Model

In step Ⅰ, GTS retains the original data for building primitive surfaces in two directories: {name}_solid and {name}_liquid. After entropy calibration, derived surface data is stored in twophase.

In step Ⅱ, for a single user-defined pressure value, the fitting data is kept in the directory: {name}_{pressure_value}_melting_data, during obtaining melting data. For a user-defined pressure range, the fitting data is kept in the directory: {name}_{min}_{max}_melting_data.

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Requirements

• Python version: 3.11.4 or higher
• Dependencies: Listed in requirements.txt

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Contribution

Contributions are welcome! If you have suggestions or improvements, please feel free to contact us.

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License

This project is licensed under the GNU General Public License v3.

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Contact

Authors:

• Kun Yin ([e-mail])
• Xuan Zhao