StatMechGlass 0.1.5
Calculates structure of oxide glasses using statistical mechanics
Requires Python: >=3.6
Keywords: glass,statistical mechanics

# 1. Introduction

This python package uses statistical mechanics-based modeling
to accurately predict the short-range order structural distribution
in oxide glasses. To make the predictions, the model requires interaction
enthalpies obtained by fitting to experimental data (typically obtained with
NMR spectroscopy techniques).

The package is designed for building a
library of enthalpies by providing relevant data to the package.

For a detailed guide, please refer to "the article" (will be filed when published).
Any bugs or questions, do not hesitate to contact msb@bio.aau.dk or mos@bio.aau.dk

# 2. Package format

The basic format of the package follows:

StatMechGlass  
  .  
  ├── Data  
  │   ├── SiB  
  │   │   ├── Na.csv  
  │   └── SiO2  
  │       ├── Na.csv  
  │       ├── Na_Tg.csv  
  ├── Parameters  
  │   ├── MF  
  │   │   ├── BAl.csv  
  │   │   └── SiB.csv  
  │   └── SiO2  
  │       ├── K.csv  
  │       └── Na.csv  
  ├── stat_mech_module  
  │   ├── `__init__`.py  
  │   ├── stat_mech_borate.py  
  │   ├── stat_mech_phosphate.py  
  │   └── stat_mech_silicate.py  
  ├── `__init__`.py   
  ├── stat_mech_glass.py  

Here, experimentally obtained data should be placed in the /Data directory.
The /parameter directory is where the package will automatically
store the enthalpies obtained by fitting the provided data. Some enthalpies are provided already.

# 3. Usage

When using the package, either type commands in the stat_mech_glass.py
file directly or import the package to a python script. It is advised to write code within `if __name__ == '__main__'`.
Alternatively, place the package in the working directory and import it with

```python
import StatMechGlass.stat_mech_glass as smg
```
or import with pip:

```python
pip install StatMechGlass
from StatMechGlass import stat_mech_glass as smg
```

The four main functions:

```python
smg.smg_binary_par(former, modifier, it=10, path_in=None)  
smg.smg_ternary_par(formers, modifier, it=10, path_in=None)  
smg.smg_structure(val, Tg, p = None)  
smg.smg_plot(comps, free_comp, Tg, plt_save = False)  
```

## 3.1 Fitting enthalpy parameters on binary oxide glasses

When building the enthalpy database, use smg.smg_binary_par:

  1.  Place data in the Data/"Former" directory, where "Former" corresponds
      to the network forming species of the glass. Currently supported formers:  
          "SiO2", "B2O3", "P2O5"  
      The data file should be named appropriately such as "Na.csv" or "K.csv"  
      Refer to Section 4 for data file layout.

  2.  Place T<sub>g</sub> data for the same glass system in the same directory with the name:  
          "modifier"_Tg.csv  
      Here, "modifier" should be the same as in 1. such as "Na_Tg.csv" or "K_Tg.csv"
      The T<sub>g</sub> data does not need to be for the same glass compositions as the
      structural data

  3.  Execute the function
      ```python  
      smg.smg_binary_par(former, modifier, it=10)
      ```  
      Example:  
      ```python
      smg.smg_binary_par("Si", "Na", it=500)  
      ```
      500 or more iterations are advised for accurate enthalpies (refer to the
      manuscript for more details)

path_in can be used to change the path for the input data (naming convention must still be followed)

## 3.2 Fitting interaction parameters on ternary oxide glasses

When building the former/former interaction database, use smg.smg_ternary_par:

  1.  Place data in the Data/"Former""Former" directory, where "Former"
      corresponds to the network forming or intermediate specie of the glass.
      Currently supported formers and intermediates:  
          SiO<sub>2</sub>, B<sub>2</sub>O<sub>3</sub>, P<sub>2</sub>O<sub>5</sub>, Al<sub>2</sub>O<sub>5</sub>  
      Here, the folder must be named according to the naming convention (section 4):  
          "SiB", "BP", "PSi", "AlB"  
      The data file should be named appropriately such as "Na.csv" or "K.csv"

  2.  T<sub>g</sub> data should be provided for each glass in the data file.
      Refer to section 4 for clarification on data file content

  3.  Execute the function  
      ```python
      smg.smg_ternary_par(formers, modifier, it=10)  
      ```
      Example:  
      ```python
      smg.smg_ternary_par(["Si", "B"], "Na", it=100)  
      ```
      100 or more iterations are advised for accurate parameter (refer to the
      manuscript for more details)

path_in can be used to change the path for the input data (naming convention must still be followed)

## 3.3 Predicting the structural distribution in a given composition

The number of compositions to be predicted by the model increases exponentially
when building the enthalpy database. This is due to the tranferability of the
interaction enthalpies. That is, enthalpies established from Na<sub>2</sub>O-SiO<sub>2</sub> and Na<sub>2</sub>O-B<sub>2</sub>O<sub>3</sub>
glasses may also be used to predict any Na<sub>2</sub>O-B<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub> composition.  

When using the model to predict structural distributions, use smg.smg_structure:

  1.  Define the glass composition using python directory  
      Example:  
      ```python
      glass_comp = {"Si": 25, "B": 25, "Na": 25, "K":25}  
      ```
  2.  Run the function with a defined T<sub>g</sub>
      Example:  
      ```python
      results = smg.smg_structure(glass_comp, 700)  
      ```

This way, users may easily build a database of structures from a large set of
glass compositions

## 3.4 Simple 2D plotting

As glass compositions may consist of many different elements, smg.smg_structure
can be used to return structures which the user may plot themselves. For simple
visualization, the smg.smg_plot function may be used:

  1.  Define the glass composition using python directory  
      Example:  
      ```python
      glass_comp = {"Si": 25, "B": 25, "Na": 0}  
      ```
      Alternatively, leave out the free component:  
      ```python
      glass_comp = {"Si": 25, "B": 25}  
      ```
  2.  Run the function with a defined T<sub>g</sub> and free component  
      Example:  
      ```python
      smg.smg_plot(glass_comp, "Na", 800, plt_save = True)  
      ```
      Set plt_save to True for saving the plot as .png file  

This will make a plot of 25SiO<sub>2</sub>-25B<sub>2</sub>O<sub>3</sub> as a function of Na<sub>2</sub>O content.

# 4. Naming convention  

For the script to locate files, parameters and functions, a certain naming
convention was introduced which must be followed:

## 4.1 Network formers and modifiers

When calling network formers in any function these are abbreviated to their
basic atom:  
"Si", "B", "Al", "P"  
Example:  
25SiO<sub>2</sub>-25B<sub>2</sub>O<sub>3</sub>-50Na<sub>2</sub>O should be {"Si": 25, "B": 25, "Na": 50}. Note that the
glass contains 2 boron atoms for each silicon atom but in the naming convention
they seem to contain the same number of atoms.

When using modifiers in the functions, these should be named according to the data
files provided by the user. If the data file is named "Na.csv", "Na" should be used
in the functions.

## 4.2 Datafiles

All data files should consist of numbers only. No letters

### 4.2.1 Binary oxide glass data  

All binary oxide glass data files must contain the modifier concentration in the
first column and the structure distributions in the following columns:

modifier_mol%,former_structure1,former_structure2,...former_structureN

Example for Na<sub>2</sub>O-SiO<sub>2</sub> data:  
Na<sub>2</sub>O%,Si<sup>4</sup>%,Si<sup>3</sup>%,Si<sup>2</sup>%,Si<sup>1</sup>%,Si<sup>0</sup>%  
Example with numbers:  

20,50,48,2,0,0  
25,38,61,1,0,0  
28.6,27,68,5,0,0  
33.3,11,79,10,0,0  

The structures reported depend on the network forming species:  

SiO<sub>2</sub>:  
Si<sup>4</sup>,Si<sup>3</sup>,Si<sup>2</sup>,Si<sup>1</sup>,Si<sup>0</sup>  

B<sub>2</sub>O<sub>3</sub>:  
B<sup>4</sup>  

P<sub>2</sub>O<sub>5</sub>:  
P<sup>3</sup>,P<sup>2</sup>,P<sup>1</sup>,P<sup>0</sup>  

Al<sub>2</sub>O<sub>3</sub>:  
Al<sup>4</sup>,Al<sup>5/6*</sup>  

`*` Note that Al<sup>5</sup> and Al<sup>6</sup> species are combined.

The T<sub>g</sub> file should contain:  
modifier_mol%,T<sub>g</sub>

### 4.2.2 Ternary oxide glass data  

All ternary oxide glass data files must contain "modifier concentration, first former concentration,
second former concentration, T<sub>g</sub>" in columns 1, 2, 3, and 4, respectively:

modifier_mol%,former1_mol%,former2_mol%,T<sub>g</sub>,former1_structures,former2_structures.  

The structures provided should follow the convention explained in Section 4.2.1 and be in order of
network forming species.  
Example data file for smg.smg_ternary_par(["Si", "B"], "Na", it=100):  
Na<sub>2</sub>O%,SiO<sub>2</sub>%,B<sub>2</sub>O<sub>3</sub>%,T<sub>g</sub>,Si<sup>4</sup>,Si<sup>3</sup>,Si<sup>2</sup>,Si<sup>1</sup>,Si<sup>0</sup>,B<sup>4</sup>  

Example for smg.smg_ternary_par(["B", "Si"], "Na", it=100):  
Na<sub>2</sub>O%,B<sub>2</sub>O<sub>3</sub>%,SiO<sub>2</sub>%,T<sub>g</sub>,B<sup>4</sup>,Si<sup>4</sup>,Si<sup>3</sup>,Si<sup>2</sup>,Si<sup>1</sup>,Si<sup>0</sup>  

# 5. Final remarks

Thank you for using the software!  
Upon building on the software or enthalpy database, you are encouraged to make a pull request by first making a seperate branch. Make sure to describe the change in detain and how you tested the change.
Possible changes could include: adding new data or parameters to the database, building upon the modules to include more glass families, or general bug fixes/improvements.

Thanks,  
Mikkel Bødker, msb@bio.aau.dk  
Oxide Glass Chemistry Group, Department of Chemistry and Bioscience, Aalborg University, Denmark